SMTL ID : 8jut.1

rat megalin RAP complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

14 x UNK- UNK- UNK- UNK- UNK- UNK: unclear peptide(Non-covalent)

UNK-UNK-UNK-UNK-UNK-UNK.1: 4 residues within 4Å: Chain A: R.512, W.557, W.618, D.1132 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.557 Hydrogen bonds: A:R.512, A:R.512 UNK-UNK-UNK-UNK-UNK-UNK.2: 7 residues within 4Å: Chain A: F.741, R.828, W.844, W.870, N.872, H.914, W.930 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.741, A:W.844, A:W.870 Hydrogen bonds: A:R.828, A:R.828, A:N.872, A:N.872 UNK-UNK-UNK-UNK-UNK-UNK.3: 7 residues within 4Å: Chain A: E.1513, R.1556, W.1574, W.1600, A.1618, H.1645, R.1661 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.1574, A:W.1600, A:W.1600, A:W.1600, A:A.1618 Hydrogen bonds: A:R.1556, A:R.1556, A:R.1661, A:R.1661 UNK-UNK-UNK-UNK-UNK-UNK.4: 6 residues within 4Å: Chain A: Y.1782, H.1891, H.1921, E.1923, W.1965 Ligands: NI.126 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.1921 UNK-UNK-UNK-UNK-UNK-UNK.5: 8 residues within 4Å: Chain A: L.2071, N.2097, F.2115, R.2149, R.2194, Y.2210, R.2296, R.2325 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.2071 Hydrogen bonds: A:N.2097, A:N.2146, A:R.2149, A:R.2149, A:Y.2210, A:Y.2210, A:R.2325 Salt bridges: A:R.2149, A:R.2194, A:R.2296 UNK-UNK-UNK-UNK-UNK-UNK.6: 8 residues within 4Å: Chain A: I.2423, K.2439, R.2511, W.2527, W.2553, N.2555, H.2595, F.2597 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.2423, A:W.2527 Hydrogen bonds: A:R.2511, A:R.2511, A:N.2555, A:N.2555 UNK-UNK-UNK-UNK-UNK-UNK.7: 8 residues within 4Å: Chain A: R.3326, W.3342, W.3368, N.3370, A.3386, H.3411, W.3427, R.3738 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.3342, A:W.3368 Hydrogen bonds: A:R.3326, A:R.3326, A:N.3370, A:N.3370, A:R.3738, A:R.3738 UNK-UNK-UNK-UNK-UNK-UNK.8: 4 residues within 4Å: Chain B: R.512, W.528, W.557, W.618 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.528, B:W.557 Hydrogen bonds: B:R.512, B:R.512 UNK-UNK-UNK-UNK-UNK-UNK.9: 7 residues within 4Å: Chain B: E.786, R.828, W.844, W.870, N.872, H.914, W.930 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.870 Hydrogen bonds: B:R.828, B:R.828, B:N.872, B:N.872 UNK-UNK-UNK-UNK-UNK-UNK.10: 6 residues within 4Å: Chain B: E.1513, R.1556, W.1574, W.1600, H.1645, R.1661 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.1574, B:W.1574, B:W.1600 Hydrogen bonds: B:R.1556, B:R.1661, B:R.1661 UNK-UNK-UNK-UNK-UNK-UNK.11: 5 residues within 4Å: Chain B: Y.1782, H.1921, E.1923, W.1965 Ligands: NI.194 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.1921 UNK-UNK-UNK-UNK-UNK-UNK.12: 10 residues within 4Å: Chain B: L.2071, N.2097, F.2115, S.2117, N.2146, R.2149, Y.2210, R.2238, R.2296, R.2325 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.2071 Hydrogen bonds: B:N.2097, B:N.2146, B:R.2149, B:R.2325 Salt bridges: B:R.2238, B:R.2296 UNK-UNK-UNK-UNK-UNK-UNK.13: 7 residues within 4Å: Chain B: I.2423, K.2439, R.2511, W.2527, W.2553, N.2555, H.2595 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.2423, B:W.2527, B:W.2553 Hydrogen bonds: B:K.2439, B:R.2511, B:N.2555, B:N.2555 UNK-UNK-UNK-UNK-UNK-UNK.14: 8 residues within 4Å: Chain B: R.3326, W.3342, W.3368, N.3370, H.3411, W.3427, R.3738, W.3739 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.3342 Hydrogen bonds: B:R.3326, B:R.3326, B:W.3368, B:N.3370, B:R.3738, B:R.3738

13 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.15: 2 residues within 4Å: Chain A: E.459, N.462 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain A: N.1436, L.1438, N.1451 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain A: N.1551 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain A: H.1673, N.1676 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain A: F.1792, N.1811 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 1 residues within 4Å: Chain A: N.2548 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 3 residues within 4Å: Chain A: F.1062, N.1063, N.1064 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 4 residues within 4Å: Chain B: N.1436, N.1451, T.1453, N.1458 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 2 residues within 4Å: Chain B: K.1550, N.1551 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 3 residues within 4Å: Chain B: H.1673, G.1675, N.1676 No protein-ligand interaction detected (PLIP) NAG-NAG.44: 1 residues within 4Å: Chain B: N.1811 No protein-ligand interaction detected (PLIP) NAG-NAG.46: 5 residues within 4Å: Chain B: N.2396, N.2397, G.2420, T.2421, T.2636 No protein-ligand interaction detected (PLIP) NAG-NAG.47: 2 residues within 4Å: Chain B: P.2545, N.2548 No protein-ligand interaction detected (PLIP)

12 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.16: 5 residues within 4Å: Chain A: D.388, S.389, F.390, A.652, N.657 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.389 NAG-NAG-BMA-MAN-MAN.22: 6 residues within 4Å: Chain A: N.1733, V.1742, R.1743, Q.1746, L.1762, D.1763 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.1763 Hydrogen bonds: A:L.1762 NAG-NAG-BMA-MAN-MAN.24: 7 residues within 4Å: Chain A: N.2107, F.2109, K.2129, N.2134, I.2177, N.2178 Ligands: NAG.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.2129 NAG-NAG-BMA-MAN-MAN.29: 5 residues within 4Å: Chain A: E.3240, R.3242, F.3257, N.3259, T.3261 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.3240, A:F.3257 NAG-NAG-BMA-MAN-MAN.32: 4 residues within 4Å: Chain A: D.3564, N.3566, A.3581, F.3860 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.33: 6 residues within 4Å: Chain A: F.3838, P.3839, N.3840, T.3842, P.3845, A.3846 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.3838, A:P.3845 Hydrogen bonds: A:A.3846 NAG-NAG-BMA-MAN-MAN.34: 10 residues within 4Å: Chain A: P.4055, L.4057, N.4070, S.4072, S.4073, N.4124, F.4125, E.4126, Y.4407, G.4415 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.43: 4 residues within 4Å: Chain B: N.1733, Q.1746, S.1761, F.1973 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.50: 4 residues within 4Å: Chain B: E.3240, K.3241, F.3257, N.3259 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.3240, B:F.3257 NAG-NAG-BMA-MAN-MAN.53: 4 residues within 4Å: Chain B: D.3564, N.3566, A.3581, F.3860 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.54: 8 residues within 4Å: Chain B: P.3551, H.3552, R.3563, F.3838, N.3840, T.3842, P.3845, A.3846 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:H.3552, B:F.3838, B:P.3845 Hydrogen bonds: B:A.3846 NAG-NAG-BMA-MAN-MAN.58: 5 residues within 4Å: Chain B: D.388, S.389, F.390, Q.433, N.657 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.389

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.17: 3 residues within 4Å: Chain A: K.849, N.865, H.1254 No protein-ligand interaction detected (PLIP)

10 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.19: 3 residues within 4Å: Chain A: F.1495, N.1497, T.1499 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 2 residues within 4Å: Chain A: H.3126, N.3127 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 5 residues within 4Å: Chain A: Y.3202, N.3213, I.3224, L.3258, K.3260 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 1 residues within 4Å: Chain A: N.3317 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 7 residues within 4Å: Chain A: H.3336, R.3350, N.3357, S.3359, E.3397, A.3486, G.3487 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.35: 7 residues within 4Å: Chain A: V.4035, D.4036, L.4241, N.4329, S.4331, V.4332 Chain B: G.78 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.38: 3 residues within 4Å: Chain B: P.862, N.865, H.1254 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.40: 3 residues within 4Å: Chain B: F.1495, N.1497, T.1499 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.51: 1 residues within 4Å: Chain B: N.3317 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.52: 6 residues within 4Å: Chain B: H.3336, R.3350, N.3357, S.3359, E.3397, A.3486 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.25: 3 residues within 4Å: Chain A: N.2396, N.2397, G.2420 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 2 residues within 4Å: Chain B: E.459, N.462 No protein-ligand interaction detected (PLIP) NAG-NAG.57: 4 residues within 4Å: Chain B: Q.1058, F.1062, N.1063, N.1064 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1063

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.45: 8 residues within 4Å: Chain B: D.2104, N.2107, F.2109, R.2127, K.2129, I.2177, N.2178 Ligands: NAG.129 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.2107, B:K.2129 NAG-NAG-BMA-MAN-MAN.55: 11 residues within 4Å: Chain B: S.4054, P.4055, N.4070, S.4072, S.4073, E.4126, H.4387, Y.4407, E.4413, V.4414, G.4415 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.4126

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.48: 3 residues within 4Å: Chain B: D.3125, H.3126, N.3127 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.49: 5 residues within 4Å: Chain B: Y.3202, N.3213, I.3224, L.3258, K.3260 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.56: 6 residues within 4Å: Chain B: V.4035, D.4036, L.4241, N.4329, S.4331, V.4332 No protein-ligand interaction detected (PLIP)

22 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.59: 2 residues within 4Å: Chain A: N.338, N.340 Ligand excluded by PLIP NAG.60: 1 residues within 4Å: Chain A: N.1384 Ligand excluded by PLIP NAG.61: 4 residues within 4Å: Chain A: S.2133, N.2134 Ligands: NAG-NAG-BMA-MAN-MAN.24, NAG-NAG-BMA-MAN-MAN.24 Ligand excluded by PLIP NAG.62: 1 residues within 4Å: Chain A: N.2225 Ligand excluded by PLIP NAG.63: 2 residues within 4Å: Chain A: I.2466, N.2488 Ligand excluded by PLIP NAG.64: 1 residues within 4Å: Chain A: N.2782 Ligand excluded by PLIP NAG.65: 2 residues within 4Å: Chain A: N.2810, D.2811 Ligand excluded by PLIP NAG.66: 3 residues within 4Å: Chain A: L.3446, V.3447, N.3448 Ligand excluded by PLIP NAG.67: 1 residues within 4Å: Chain A: N.3682 Ligand excluded by PLIP NAG.68: 2 residues within 4Å: Chain A: N.3980, R.3994 Ligand excluded by PLIP NAG.69: 2 residues within 4Å: Chain A: N.1187, C.1188 Ligand excluded by PLIP NAG.127: 3 residues within 4Å: Chain B: N.338, N.340, I.346 Ligand excluded by PLIP NAG.128: 1 residues within 4Å: Chain B: N.1384 Ligand excluded by PLIP NAG.129: 2 residues within 4Å: Chain B: N.2134 Ligands: NAG-NAG-BMA-MAN-MAN.45 Ligand excluded by PLIP NAG.130: 2 residues within 4Å: Chain B: F.2220, N.2225 Ligand excluded by PLIP NAG.131: 3 residues within 4Å: Chain B: G.2467, N.2488, E.2681 Ligand excluded by PLIP NAG.132: 1 residues within 4Å: Chain B: N.2782 Ligand excluded by PLIP NAG.133: 1 residues within 4Å: Chain B: N.2810 Ligand excluded by PLIP NAG.134: 1 residues within 4Å: Chain B: N.3448 Ligand excluded by PLIP NAG.135: 2 residues within 4Å: Chain B: H.3068, N.3682 Ligand excluded by PLIP NAG.136: 2 residues within 4Å: Chain B: N.3980, R.3994 Ligand excluded by PLIP NAG.137: 1 residues within 4Å: Chain B: N.1187 Ligand excluded by PLIP

24 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Post Translational Modification)

A2G.70: 4 residues within 4Å: Chain A: T.221, C.222, G.223, T.679 Ligand excluded by PLIP A2G.71: 6 residues within 4Å: Chain A: N.780, R.781, Y.1001, T.1022, Q.1023, Q.1024 Ligand excluded by PLIP A2G.72: 1 residues within 4Å: Chain A: T.1065 Ligand excluded by PLIP A2G.73: 2 residues within 4Å: Chain A: S.1107, T.1109 Ligand excluded by PLIP A2G.74: 2 residues within 4Å: Chain A: T.1149, C.1150 Ligand excluded by PLIP A2G.75: 2 residues within 4Å: Chain A: T.1225, P.1227 Ligand excluded by PLIP A2G.76: 2 residues within 4Å: Chain A: T.1271, C.1272 Ligand excluded by PLIP A2G.77: 1 residues within 4Å: Chain A: T.2741 Ligand excluded by PLIP A2G.78: 3 residues within 4Å: Chain A: T.3636, C.3637, R.3638 Ligand excluded by PLIP A2G.79: 2 residues within 4Å: Chain A: T.3799, C.3800 Ligand excluded by PLIP A2G.80: 5 residues within 4Å: Chain A: T.3836, F.3838, P.3839, N.3840, G.3841 Ligand excluded by PLIP A2G.81: 3 residues within 4Å: Chain A: T.1103, A.1105, T.1106 Ligand excluded by PLIP A2G.138: 3 residues within 4Å: Chain B: T.221, G.223, T.679 Ligand excluded by PLIP A2G.139: 5 residues within 4Å: Chain B: N.780, R.781, Y.1001, T.1022, Q.1023 Ligand excluded by PLIP A2G.140: 3 residues within 4Å: Chain B: N.1063, T.1065, C.1066 Ligand excluded by PLIP A2G.141: 1 residues within 4Å: Chain B: T.1109 Ligand excluded by PLIP A2G.142: 3 residues within 4Å: Chain B: G.1148, T.1149, Q.1151 Ligand excluded by PLIP A2G.143: 3 residues within 4Å: Chain B: T.1225, R.1226, P.1227 Ligand excluded by PLIP A2G.144: 3 residues within 4Å: Chain B: T.1271, C.1272, S.1273 Ligand excluded by PLIP A2G.145: 3 residues within 4Å: Chain A: Q.1009 Chain B: H.2740, T.2741 Ligand excluded by PLIP A2G.146: 4 residues within 4Å: Chain B: T.3636, C.3637, R.3638, P.3639 Ligand excluded by PLIP A2G.147: 2 residues within 4Å: Chain B: T.3799, C.3800 Ligand excluded by PLIP A2G.148: 4 residues within 4Å: Chain B: T.3836, R.3837, P.3839, G.3841 Ligand excluded by PLIP A2G.149: 3 residues within 4Å: Chain B: T.1103, A.1105, T.1106 Ligand excluded by PLIP

88 x CA: CALCIUM ION(Non-covalent)

CA.82: 6 residues within 4Å: Chain A: W.45, D.48, T.50, D.52, D.58, E.59 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:W.45, A:D.48, A:T.50, A:D.52, A:D.58, A:E.59 CA.83: 6 residues within 4Å: Chain A: W.85, D.88, D.90, D.92, E.99 Chain B: K.4027 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:W.85, A:D.90, A:D.92, A:E.99 CA.84: 6 residues within 4Å: Chain A: Y.200, D.203, D.205, D.207, D.213, E.214 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:Y.200, A:D.203, A:D.205, A:D.207, A:D.213, A:E.214 CA.85: 6 residues within 4Å: Chain A: W.239, D.242, D.244, D.246, D.252, E.253 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:W.239, A:D.242, A:D.244, A:D.246, A:D.252, A:E.253 CA.86: 7 residues within 4Å: Chain A: K.283, C.285, D.286, V.288, D.290, D.296, E.297 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:K.283, A:D.286, A:V.288, A:D.296, A:E.297 CA.87: 4 residues within 4Å: Chain A: S.575, D.578, P.601, T.1131 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:S.575, A:D.578, A:P.601, A:T.1131 CA.88: 3 residues within 4Å: Chain A: A.888, D.891, T.913 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:A.888, A:T.913 CA.89: 6 residues within 4Å: Chain A: F.1042, D.1045, V.1047, D.1049, D.1055, E.1056 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:F.1042, A:D.1045, A:V.1047, A:D.1049, A:E.1056 CA.90: 7 residues within 4Å: Chain A: R.422, W.1084, D.1087, Q.1089, D.1091, D.1097, E.1098 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:W.1084, A:D.1087, A:Q.1089, A:D.1091, A:D.1097, A:E.1098 CA.91: 6 residues within 4Å: Chain A: W.1127, D.1130, D.1132, D.1134, D.1140, E.1141 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.1127, A:D.1130, A:D.1132, A:D.1134, A:D.1140 CA.92: 6 residues within 4Å: Chain A: Y.1167, D.1170, D.1172, D.1174, D.1180, E.1181 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:Y.1167, A:D.1170, A:D.1172, A:D.1174, A:E.1181 CA.93: 6 residues within 4Å: Chain A: Y.1206, D.1209, V.1211, D.1213, D.1219, E.1220 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:Y.1206, A:V.1211, A:D.1213, A:D.1219, A:E.1220 CA.94: 6 residues within 4Å: Chain A: W.1249, D.1252, H.1254, D.1256, D.1262, E.1263 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.1249, A:D.1252, A:H.1254, A:D.1262, A:E.1263 CA.95: 6 residues within 4Å: Chain A: W.1289, D.1292, D.1294, D.1296, D.1302, E.1303 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.1289, A:D.1292, A:D.1294, A:D.1296, A:D.1302 CA.96: 7 residues within 4Å: Chain A: A.1331, C.1333, D.1334, V.1336, D.1338, D.1344, E.1345 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.1334, A:V.1336, A:D.1338, A:D.1344, A:E.1345 CA.97: 8 residues within 4Å: Chain A: D.1391, I.1392, E.1394, N.1407, M.1408, R.1409, G.1410, S.1411 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.1391, A:E.1394, A:E.1394, A:M.1408, A:S.1411 CA.98: 3 residues within 4Å: Chain A: A.1618, D.1621, H.1644 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:A.1618, A:D.1621, A:D.1621, A:H.1644 CA.99: 5 residues within 4Å: Chain A: D.2254, D.2257, P.2279 Chain B: E.1982, N.2001 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.2254, A:D.2257, A:P.2279 CA.100: 6 residues within 4Å: Chain A: W.2718, D.2721, D.2723, D.2725, D.2731, E.2732 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.2718, A:D.2723, A:D.2725, A:D.2731, A:E.2732 CA.101: 6 residues within 4Å: Chain A: Y.2759, D.2762, Y.2764, D.2766, D.2772, E.2773 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:Y.2759, A:D.2762, A:Y.2764, A:D.2766, A:D.2772, A:E.2773 CA.102: 6 residues within 4Å: Chain A: Y.2799, N.2802, I.2804, N.2806, D.2814, E.2815 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:Y.2799, A:I.2804, A:D.2814, A:E.2815 CA.103: 5 residues within 4Å: Chain A: F.2841, D.2844, D.2846, D.2848, D.2854 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.2844, A:D.2846, A:D.2848, A:D.2854, A:D.2854 CA.104: 9 residues within 4Å: Chain A: W.2883, F.2884, C.2885, D.2886, E.2888, A.2889, D.2890, D.2896, E.2897 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.2886, A:E.2888, A:D.2890, A:D.2896, A:E.2897 CA.105: 6 residues within 4Å: Chain A: W.2925, D.2928, D.2930, D.2932, D.2938, E.2939 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:W.2925, A:D.2928, A:D.2930, A:D.2932, A:D.2938, A:E.2939 CA.106: 6 residues within 4Å: Chain A: W.2972, D.2975, D.2977, D.2979, D.2985, E.2986 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.2972, A:D.2977, A:D.2979, A:D.2985, A:E.2986 CA.107: 6 residues within 4Å: Chain A: F.3012, D.3015, R.3017, D.3019, D.3025, E.3026 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.3015, A:R.3017, A:D.3019, A:D.3025, A:E.3026 CA.108: 7 residues within 4Å: Chain A: F.3051, C.3053, D.3054, D.3056, D.3058, D.3064, E.3065 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.3054, A:D.3056, A:D.3058, A:D.3064, A:E.3065 CA.109: 6 residues within 4Å: Chain A: R.3094, N.3097, V.3099, D.3101, D.3107, E.3108 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:R.3094, A:V.3099, A:D.3101, A:D.3101, A:E.3108 CA.110: 7 residues within 4Å: Chain A: D.3154, I.3155, E.3157, N.3171, V.3172, G.3174, S.3175 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.3157, A:E.3157, A:V.3172, A:S.3175 CA.111: 3 residues within 4Å: Chain A: A.3291, D.3294, E.3323 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:A.3291, A:D.3294, A:E.3323 CA.112: 2 residues within 4Å: Chain A: V.3344, E.3367 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:V.3344, A:E.3367 CA.113: 3 residues within 4Å: Chain A: A.3386, H.3387, P.3410 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:A.3386, A:H.3387 CA.114: 6 residues within 4Å: Chain A: W.3532, D.3535, Q.3537, D.3539, D.3545, E.3546 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.3532, A:D.3535, A:Q.3537, A:D.3539, A:E.3546 CA.115: 7 residues within 4Å: Chain A: A.3572, N.3575, R.3577, Q.3578, D.3579, D.3585, E.3586 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:A.3572, A:R.3577, A:D.3579, A:D.3585, A:E.3586 CA.116: 6 residues within 4Å: Chain A: W.3613, D.3616, V.3618, D.3620, D.3626, E.3627 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.3613, A:V.3618, A:D.3620, A:D.3626, A:E.3627 CA.117: 6 residues within 4Å: Chain A: W.3654, D.3657, D.3659, D.3661, D.3667, E.3668 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:W.3654, A:D.3657, A:D.3659, A:D.3661, A:D.3667, A:E.3668 CA.118: 6 residues within 4Å: Chain A: A.3699, N.3702, F.3704, D.3706, D.3712, E.3713 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:A.3699, A:F.3704, A:D.3706, A:D.3712, A:E.3713 CA.119: 6 residues within 4Å: Chain A: W.3739, D.3742, T.3744, D.3746, D.3752, E.3753 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.3739, A:T.3744, A:D.3746, A:D.3752, A:E.3753 CA.120: 6 residues within 4Å: Chain A: W.3778, D.3781, E.3783, D.3785, D.3791, E.3792 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.3778, A:D.3781, A:E.3783, A:D.3785, A:E.3792 CA.121: 6 residues within 4Å: Chain A: L.3817, D.3820, R.3822, D.3824, D.3830, E.3831 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:L.3817, A:D.3820, A:R.3822, A:D.3824, A:D.3830, A:E.3831 CA.122: 8 residues within 4Å: Chain A: W.3861, C.3863, D.3864, G.3865, E.3866, D.3868, D.3874, E.3875 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.3864, A:E.3866, A:D.3868, A:D.3874, A:E.3875 CA.123: 6 residues within 4Å: Chain A: Q.3903, C.3905, N.3906, V.3908, D.3916, E.3917 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:Q.3903, A:V.3908, A:D.3916, A:D.3916, A:E.3917 CA.124: 6 residues within 4Å: Chain A: Y.3947, D.3950, V.3952, D.3954, D.3960, E.3961 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:Y.3947, A:V.3952, A:D.3954, A:D.3960, A:E.3961 CA.125: 7 residues within 4Å: Chain A: D.4009, I.4010, E.4012, N.4025, S.4026, G.4028, S.4029 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.4009, A:E.4012, A:E.4012, A:S.4026, A:S.4029 CA.150: 7 residues within 4Å: Chain B: W.45, C.47, D.48, T.50, D.52, D.58, E.59 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.45, B:D.48, B:T.50, B:D.52, B:D.58 CA.151: 6 residues within 4Å: Chain B: W.85, D.88, D.90, D.92, D.98, E.99 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.85, B:D.88, B:D.90, B:D.98, B:E.99 CA.152: 8 residues within 4Å: Chain B: Y.200, V.201, C.202, D.203, D.205, D.207, D.213, E.214 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.203, B:D.205, B:D.207, B:D.213, B:E.214 CA.153: 6 residues within 4Å: Chain B: W.239, D.242, D.244, D.246, D.252, E.253 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.239, B:D.244, B:D.246, B:D.252, B:E.253 CA.154: 7 residues within 4Å: Chain B: K.283, C.285, D.286, V.288, D.290, D.296, E.297 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.286, B:V.288, B:D.290, B:D.296, B:E.297 CA.155: 6 residues within 4Å: Chain B: S.575, R.576, D.578, P.601, T.1131, D.1132 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.575, B:D.578, B:T.1131 CA.156: 4 residues within 4Å: Chain B: A.888, F.889, D.891, T.913 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:A.888, B:D.891 CA.157: 6 residues within 4Å: Chain B: F.1042, D.1045, V.1047, D.1049, D.1055, E.1056 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:F.1042, B:D.1045, B:V.1047, B:D.1049, B:D.1055, B:E.1056 CA.158: 6 residues within 4Å: Chain B: W.1084, D.1087, Q.1089, D.1091, D.1097, E.1098 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.1084, B:D.1087, B:Q.1089, B:D.1097, B:E.1098 CA.159: 6 residues within 4Å: Chain B: W.1127, D.1130, D.1132, D.1134, D.1140, E.1141 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.1127, B:D.1130, B:D.1134, B:D.1140, B:E.1141 CA.160: 6 residues within 4Å: Chain B: Y.1167, D.1170, D.1172, D.1174, D.1180, E.1181 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:Y.1167, B:D.1172, B:D.1174, B:D.1180, B:E.1181 CA.161: 6 residues within 4Å: Chain B: Y.1206, D.1209, V.1211, D.1213, D.1219, E.1220 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:Y.1206, B:D.1209, B:V.1211, B:D.1213, B:D.1219, B:E.1220 CA.162: 6 residues within 4Å: Chain B: W.1249, D.1252, H.1254, D.1256, D.1262, E.1263 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.1249, B:D.1252, B:H.1254, B:D.1256, B:D.1262 CA.163: 7 residues within 4Å: Chain B: W.1289, C.1291, D.1292, D.1294, D.1296, D.1302, E.1303 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.1289, B:D.1292, B:D.1294, B:D.1296, B:D.1302 CA.164: 6 residues within 4Å: Chain B: A.1331, D.1334, V.1336, D.1338, D.1344, E.1345 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:A.1331, B:D.1334, B:V.1336, B:D.1338, B:D.1344, B:E.1345 CA.165: 7 residues within 4Å: Chain B: D.1391, I.1392, E.1394, N.1407, M.1408, G.1410, S.1411 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.1391, B:E.1394, B:E.1394, B:M.1408, B:S.1411 CA.166: 3 residues within 4Å: Chain B: A.1618, D.1621, H.1644 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:A.1618, B:D.1621, B:D.1621, B:H.1644 CA.167: 5 residues within 4Å: Chain A: E.1982, N.2001 Chain B: D.2254, D.2257, P.2279 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.2254, B:D.2257, B:P.2279 CA.168: 6 residues within 4Å: Chain B: W.2718, D.2721, D.2723, D.2725, D.2731, E.2732 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:W.2718, B:D.2721, B:D.2723, B:D.2725, B:D.2731, B:E.2732 CA.169: 6 residues within 4Å: Chain B: Y.2759, D.2762, Y.2764, D.2766, D.2772, E.2773 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:Y.2759, B:D.2762, B:Y.2764, B:D.2766, B:D.2772, B:E.2773 CA.170: 6 residues within 4Å: Chain B: Y.2799, N.2802, I.2804, N.2806, D.2814, E.2815 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:Y.2799, B:I.2804, B:D.2814, B:E.2815 CA.171: 7 residues within 4Å: Chain B: L.2842, C.2843, D.2844, D.2846, D.2848, D.2854, E.2855 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.2844, B:D.2846, B:D.2848, B:D.2854, B:E.2855 CA.172: 5 residues within 4Å: Chain B: W.2883, E.2888, D.2890, D.2896, E.2897 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.2883, B:E.2888, B:D.2896, B:D.2896, B:E.2897 CA.173: 7 residues within 4Å: Chain B: W.2925, D.2928, G.2929, D.2930, D.2932, D.2938, E.2939 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.2925, B:D.2928, B:D.2930, B:D.2938, B:E.2939 CA.174: 6 residues within 4Å: Chain B: W.2972, D.2975, D.2977, D.2979, D.2985, E.2986 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.2972, B:D.2975, B:D.2977, B:D.2979, B:D.2985 CA.175: 6 residues within 4Å: Chain B: F.3012, D.3015, R.3017, D.3019, D.3025, E.3026 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:F.3012, B:D.3015, B:D.3019, B:D.3025, B:E.3026 CA.176: 6 residues within 4Å: Chain B: F.3051, D.3054, D.3056, D.3058, D.3064, E.3065 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.3054, B:D.3056, B:D.3058, B:D.3064, B:E.3065 CA.177: 6 residues within 4Å: Chain B: R.3094, N.3097, V.3099, D.3101, D.3107, E.3108 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:R.3094, B:V.3099, B:D.3101, B:D.3107, B:E.3108 CA.178: 7 residues within 4Å: Chain B: D.3154, I.3155, E.3157, N.3171, V.3172, G.3174, S.3175 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.3154, B:I.3155, B:E.3157, B:E.3157, B:V.3172 CA.179: 3 residues within 4Å: Chain B: A.3291, D.3294, E.3323 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:A.3291, B:D.3294, B:E.3323 CA.180: 3 residues within 4Å: Chain B: V.3344, E.3367, T.3684 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:V.3344, B:E.3367, B:T.3684 CA.181: 3 residues within 4Å: Chain B: A.3386, H.3387, P.3410 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:A.3386 CA.182: 6 residues within 4Å: Chain B: W.3532, D.3535, Q.3537, D.3539, D.3545, E.3546 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.3535, B:Q.3537, B:D.3539, B:D.3545, B:E.3546 CA.183: 6 residues within 4Å: Chain B: A.3572, N.3575, R.3577, D.3579, D.3585, E.3586 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:A.3572, B:R.3577, B:D.3579, B:D.3585, B:E.3586 CA.184: 6 residues within 4Å: Chain B: W.3613, D.3616, V.3618, D.3620, D.3626, E.3627 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.3613, B:D.3616, B:V.3618, B:D.3620, B:E.3627 CA.185: 6 residues within 4Å: Chain B: W.3654, D.3657, D.3659, D.3661, D.3667, E.3668 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.3657, B:D.3659, B:D.3661, B:D.3667, B:E.3668 CA.186: 6 residues within 4Å: Chain B: A.3699, N.3702, F.3704, D.3706, D.3712, E.3713 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:A.3699, B:F.3704, B:D.3706, B:D.3712, B:E.3713 CA.187: 6 residues within 4Å: Chain B: W.3739, D.3742, T.3744, D.3746, D.3752, E.3753 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.3742, B:T.3744, B:D.3746, B:D.3752, B:E.3753 CA.188: 6 residues within 4Å: Chain B: W.3778, D.3781, E.3783, D.3785, D.3791, E.3792 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.3778, B:D.3781, B:E.3783, B:D.3785, B:D.3791 CA.189: 6 residues within 4Å: Chain B: L.3817, D.3820, R.3822, D.3824, D.3830, E.3831 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:L.3817, B:D.3820, B:R.3822, B:D.3824, B:D.3830, B:E.3831 CA.190: 6 residues within 4Å: Chain B: W.3861, D.3864, E.3866, D.3868, D.3874, E.3875 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.3861, B:D.3864, B:E.3866, B:D.3868, B:D.3874 CA.191: 6 residues within 4Å: Chain B: Q.3903, N.3906, V.3908, D.3910, D.3916, E.3917 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:Q.3903, B:V.3908, B:D.3910, B:D.3916, B:E.3917 CA.192: 6 residues within 4Å: Chain B: Y.3947, D.3950, V.3952, D.3954, D.3960, E.3961 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:Y.3947, B:D.3950, B:V.3952, B:D.3954, B:E.3961 CA.193: 7 residues within 4Å: Chain B: D.4009, I.4010, E.4012, N.4025, S.4026, G.4028, S.4029 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.4009, B:I.4010, B:E.4012, B:E.4012, B:S.4026

2 x NI: NICKEL (II) ION(Non-covalent)

NI.126: 4 residues within 4Å: Chain A: H.1921, E.1923, H.1963 Ligands: UNK-CYS-UNK.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.1921, A:E.1923, A:H.1963 NI.194: 4 residues within 4Å: Chain B: H.1921, E.1923, H.1963 Ligands: UNK-CYS-UNK.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.1921, B:E.1923, B:H.1963

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goto, S. et al., Cryo-EM structures elucidate the multiligand receptor nature of megalin. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-06-19

Peptides

LDL receptor related protein 2: AB
Alpha-2-macroglobulin receptor-associated protein: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

LDL receptor related protein 2

Alpha-2-macroglobulin receptor-associated protein

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