SMTL ID : 8em7.1

Cryo-EM structure of LRP2 at pH 5.2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

NAG-NAG.1: 7 residues within 4Å: Chain A: N.2107, F.2109, R.2127, K.2129, I.2177, N.2178 Ligands: NAG.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.2129 NAG-NAG.2: 7 residues within 4Å: Chain B: N.2107, F.2109, R.2127, K.2129, I.2177, N.2178 Ligands: NAG.122 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.2129

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

NAG.3: 2 residues within 4Å: Chain A: N.340, N.3523 Ligand excluded by PLIP NAG.4: 4 residues within 4Å: Chain A: E.374, I.377, N.387, S.389 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain A: F.390, Q.433, A.652, N.657 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: P.862, N.865 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.1187, T.2549 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.1328 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: Y.1323, P.1340, N.1341 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.1384 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.1451, T.1453 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain A: F.1495, N.1497, T.1499, Y.2612, R.2633 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: N.1551, R.1579, E.1581, V.1592 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: R.1675, N.1676 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.1733, Q.1746 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: S.1810, N.1811 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: S.2133, N.2134 Ligands: NAG-NAG.1, NAG-NAG.1 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: F.2220, N.2225 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: N.2396, N.2397, G.2420, T.2636 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: G.2467, N.2488 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: P.2545, N.2548 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.2782 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.2810 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.2949, R.2966 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.2989 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: H.3126, N.3127 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain A: Y.3202, N.3213, I.3224, L.3258, K.3260 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: E.3240, F.3257, N.3259, T.3261 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain A: N.3317 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain A: Y.3336, R.3350, N.3357, E.3397 Ligand excluded by PLIP NAG.31: 9 residues within 4Å: Chain A: G.2929, D.2930, N.2931, M.2936, P.2963, R.3430, N.3448, T.3449, T.3450 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: D.3564, N.3566, A.3581, D.3582 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain A: N.3682 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain A: F.3838, P.3839, N.3840, A.3846 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.3969 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: Q.3979, N.3980, R.3994 Ligand excluded by PLIP NAG.37: 7 residues within 4Å: Chain A: P.4055, L.4057, N.4070, S.4072, S.4073, D.4124, E.4126 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain A: V.4035, D.4036, N.4329, S.4331, V.4332 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain A: N.178 Ligand excluded by PLIP NAG.106: 4 residues within 4Å: Chain A: C.157, Y.158, N.159, Q.162 Ligand excluded by PLIP NAG.107: 2 residues within 4Å: Chain A: N.462, N.498 Ligand excluded by PLIP NAG.108: 2 residues within 4Å: Chain B: N.340, N.3523 Ligand excluded by PLIP NAG.109: 4 residues within 4Å: Chain B: E.374, I.377, N.387, S.389 Ligand excluded by PLIP NAG.110: 4 residues within 4Å: Chain B: F.390, Q.433, A.652, N.657 Ligand excluded by PLIP NAG.111: 2 residues within 4Å: Chain B: P.862, N.865 Ligand excluded by PLIP NAG.112: 2 residues within 4Å: Chain B: N.1187, T.2549 Ligand excluded by PLIP NAG.113: 1 residues within 4Å: Chain B: N.1328 Ligand excluded by PLIP NAG.114: 3 residues within 4Å: Chain B: Y.1323, P.1340, N.1341 Ligand excluded by PLIP NAG.115: 1 residues within 4Å: Chain B: N.1384 Ligand excluded by PLIP NAG.116: 2 residues within 4Å: Chain B: N.1451, T.1453 Ligand excluded by PLIP NAG.117: 5 residues within 4Å: Chain B: F.1495, N.1497, T.1499, Y.2612, R.2633 Ligand excluded by PLIP NAG.118: 4 residues within 4Å: Chain B: N.1551, R.1579, E.1581, V.1592 Ligand excluded by PLIP NAG.119: 2 residues within 4Å: Chain B: R.1675, N.1676 Ligand excluded by PLIP NAG.120: 2 residues within 4Å: Chain B: N.1733, Q.1746 Ligand excluded by PLIP NAG.121: 2 residues within 4Å: Chain B: S.1810, N.1811 Ligand excluded by PLIP NAG.122: 4 residues within 4Å: Chain B: S.2133, N.2134 Ligands: NAG-NAG.2, NAG-NAG.2 Ligand excluded by PLIP NAG.123: 2 residues within 4Å: Chain B: F.2220, N.2225 Ligand excluded by PLIP NAG.124: 4 residues within 4Å: Chain B: N.2396, N.2397, G.2420, T.2636 Ligand excluded by PLIP NAG.125: 2 residues within 4Å: Chain B: G.2467, N.2488 Ligand excluded by PLIP NAG.126: 2 residues within 4Å: Chain B: P.2545, N.2548 Ligand excluded by PLIP NAG.127: 1 residues within 4Å: Chain B: N.2782 Ligand excluded by PLIP NAG.128: 1 residues within 4Å: Chain B: N.2810 Ligand excluded by PLIP NAG.129: 2 residues within 4Å: Chain B: N.2949, R.2966 Ligand excluded by PLIP NAG.130: 1 residues within 4Å: Chain B: N.2989 Ligand excluded by PLIP NAG.131: 2 residues within 4Å: Chain B: H.3126, N.3127 Ligand excluded by PLIP NAG.132: 5 residues within 4Å: Chain B: Y.3202, N.3213, I.3224, L.3258, K.3260 Ligand excluded by PLIP NAG.133: 4 residues within 4Å: Chain B: E.3240, F.3257, N.3259, T.3261 Ligand excluded by PLIP NAG.134: 1 residues within 4Å: Chain B: N.3317 Ligand excluded by PLIP NAG.135: 4 residues within 4Å: Chain B: Y.3336, R.3350, N.3357, E.3397 Ligand excluded by PLIP NAG.136: 9 residues within 4Å: Chain B: G.2929, D.2930, N.2931, M.2936, P.2963, R.3430, N.3448, T.3449, T.3450 Ligand excluded by PLIP NAG.137: 4 residues within 4Å: Chain B: D.3564, N.3566, A.3581, D.3582 Ligand excluded by PLIP NAG.138: 1 residues within 4Å: Chain B: N.3682 Ligand excluded by PLIP NAG.139: 4 residues within 4Å: Chain B: F.3838, P.3839, N.3840, A.3846 Ligand excluded by PLIP NAG.140: 1 residues within 4Å: Chain B: N.3969 Ligand excluded by PLIP NAG.141: 3 residues within 4Å: Chain B: Q.3979, N.3980, R.3994 Ligand excluded by PLIP NAG.142: 7 residues within 4Å: Chain B: P.4055, L.4057, N.4070, S.4072, S.4073, D.4124, E.4126 Ligand excluded by PLIP NAG.143: 5 residues within 4Å: Chain B: V.4035, D.4036, N.4329, S.4331, V.4332 Ligand excluded by PLIP NAG.146: 1 residues within 4Å: Chain B: N.178 Ligand excluded by PLIP NAG.211: 4 residues within 4Å: Chain B: C.157, Y.158, N.159, Q.162 Ligand excluded by PLIP NAG.212: 2 residues within 4Å: Chain B: N.462, N.498 Ligand excluded by PLIP

44 x NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose(Post Translational Modification)

NGA.39: 1 residues within 4Å: Chain A: S.66 Ligand excluded by PLIP NGA.40: 3 residues within 4Å: Chain A: T.107, C.108, S.109 Ligand excluded by PLIP NGA.42: 3 residues within 4Å: Chain A: T.221, C.222, G.223 Ligand excluded by PLIP NGA.43: 4 residues within 4Å: Chain A: T.1065, C.1066, S.1067, S.1068 Ligand excluded by PLIP NGA.44: 3 residues within 4Å: Chain A: P.1102, T.1103, R.1104 Ligand excluded by PLIP NGA.45: 2 residues within 4Å: Chain A: S.1108, T.1109 Ligand excluded by PLIP NGA.46: 5 residues within 4Å: Chain A: S.1147, T.1149, C.1150, H.1151, P.2442 Ligand excluded by PLIP NGA.47: 3 residues within 4Å: Chain A: T.1225, R.1226, P.1227 Ligand excluded by PLIP NGA.48: 1 residues within 4Å: Chain A: T.1271 Ligand excluded by PLIP NGA.49: 4 residues within 4Å: Chain A: R.2480, N.2500, A.2502, T.2741 Ligand excluded by PLIP NGA.50: 3 residues within 4Å: Chain A: T.2822, C.2823, Q.2824 Ligand excluded by PLIP NGA.51: 1 residues within 4Å: Chain A: T.2864 Ligand excluded by PLIP NGA.52: 3 residues within 4Å: Chain A: S.2907, C.2908, S.2909 Ligand excluded by PLIP NGA.53: 4 residues within 4Å: Chain A: L.3069, C.3070, H.3071, T.3072 Ligand excluded by PLIP NGA.54: 2 residues within 4Å: Chain A: T.3076, C.3077 Ligand excluded by PLIP NGA.55: 2 residues within 4Å: Chain A: T.3799, H.3801 Ligand excluded by PLIP NGA.56: 1 residues within 4Å: Chain A: T.3926 Ligand excluded by PLIP NGA.101: 2 residues within 4Å: Chain A: T.1308, Q.1309 Ligand excluded by PLIP NGA.102: 4 residues within 4Å: Chain A: M.1408, G.1410, S.1411, F.1412 Ligand excluded by PLIP NGA.103: 4 residues within 4Å: Chain A: G.3142, E.3157, S.3175, Y.3176 Ligand excluded by PLIP NGA.104: 2 residues within 4Å: Chain A: T.3836, G.3841 Ligand excluded by PLIP NGA.105: 4 residues within 4Å: Chain A: T.1022, C.1032, N.1033, G.1035 Ligand excluded by PLIP NGA.144: 1 residues within 4Å: Chain B: S.66 Ligand excluded by PLIP NGA.145: 3 residues within 4Å: Chain B: T.107, C.108, S.109 Ligand excluded by PLIP NGA.147: 3 residues within 4Å: Chain B: T.221, C.222, G.223 Ligand excluded by PLIP NGA.148: 4 residues within 4Å: Chain B: T.1065, C.1066, S.1067, S.1068 Ligand excluded by PLIP NGA.149: 3 residues within 4Å: Chain B: P.1102, T.1103, R.1104 Ligand excluded by PLIP NGA.150: 2 residues within 4Å: Chain B: S.1108, T.1109 Ligand excluded by PLIP NGA.151: 5 residues within 4Å: Chain B: S.1147, T.1149, C.1150, H.1151, P.2442 Ligand excluded by PLIP NGA.152: 3 residues within 4Å: Chain B: T.1225, R.1226, P.1227 Ligand excluded by PLIP NGA.153: 1 residues within 4Å: Chain B: T.1271 Ligand excluded by PLIP NGA.154: 4 residues within 4Å: Chain B: R.2480, N.2500, A.2502, T.2741 Ligand excluded by PLIP NGA.155: 3 residues within 4Å: Chain B: T.2822, C.2823, Q.2824 Ligand excluded by PLIP NGA.156: 1 residues within 4Å: Chain B: T.2864 Ligand excluded by PLIP NGA.157: 3 residues within 4Å: Chain B: S.2907, C.2908, S.2909 Ligand excluded by PLIP NGA.158: 4 residues within 4Å: Chain B: L.3069, C.3070, H.3071, T.3072 Ligand excluded by PLIP NGA.159: 2 residues within 4Å: Chain B: T.3076, C.3077 Ligand excluded by PLIP NGA.160: 2 residues within 4Å: Chain B: T.3799, H.3801 Ligand excluded by PLIP NGA.161: 1 residues within 4Å: Chain B: T.3926 Ligand excluded by PLIP NGA.206: 2 residues within 4Å: Chain B: T.1308, Q.1309 Ligand excluded by PLIP NGA.207: 4 residues within 4Å: Chain B: M.1408, G.1410, S.1411, F.1412 Ligand excluded by PLIP NGA.208: 4 residues within 4Å: Chain B: G.3142, E.3157, S.3175, Y.3176 Ligand excluded by PLIP NGA.209: 2 residues within 4Å: Chain B: T.3836, G.3841 Ligand excluded by PLIP NGA.210: 4 residues within 4Å: Chain B: T.1022, C.1032, N.1033, G.1035 Ligand excluded by PLIP

88 x CA: CALCIUM ION(Non-covalent)

CA.57: 6 residues within 4Å: Chain A: A.3572, N.3575, R.3577, 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.58: 7 residues within 4Å: Chain A: W.85, V.86, D.88, D.90, D.92, D.98, E.99 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:V.86, A:D.88, A:D.92, A:D.98, A:E.99 CA.59: 6 residues within 4Å: Chain A: Y.125, D.128, V.130, D.132, D.138, E.139 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:Y.125, A:D.128, A:V.130, A:D.132, A:D.138, A:E.139 CA.60: 7 residues within 4Å: Chain A: Q.162, K.163, D.165, K.167, D.169, D.175, E.176 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:Q.162, A:D.165, A:K.167, A:D.169, A:D.175, A:E.176 CA.61: 6 residues within 4Å: Chain A: Y.200, D.203, D.205, D.207, D.213, E.214 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.203, A:D.205, A:D.207, A:D.213, A:E.214 CA.62: 7 residues within 4Å: Chain A: W.239, D.242, D.244, D.246, D.252, E.253, K.554 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.239, A:D.244, A:D.246, A:D.252, A:E.253 CA.63: 7 residues within 4Å: Chain A: K.283, D.286, G.287, 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.64: 7 residues within 4Å: Chain A: F.1042, D.1045, V.1047, D.1048, D.1049, D.1055, E.1056 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.1045, A:V.1047, A:D.1049, A:D.1055, A:E.1056 CA.65: 7 residues within 4Å: Chain A: W.1084, D.1087, Q.1089, N.1090, D.1091, D.1097, E.1098 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.1084, A:D.1087, A:D.1091, A:D.1097, A:E.1098 CA.66: 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:D.1130, A:D.1130, A:D.1132, A:D.1134, A:E.1141 CA.67: 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.1172, A:D.1174, A:D.1180, A:E.1181 CA.68: 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:D.1209, A:V.1211, A:D.1213, A:D.1219 CA.69: 7 residues within 4Å: Chain A: W.1249, E.1250, D.1252, H.1254, D.1256, D.1262, E.1263 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.1252, A:H.1254, A:D.1256, A:D.1262, A:E.1263 CA.70: 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.71: 6 residues within 4Å: Chain A: A.1331, D.1334, V.1336, D.1338, D.1344, E.1345 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:A.1331, A:V.1336, A:D.1338, A:D.1344, A:E.1345 CA.72: 7 residues within 4Å: Chain A: W.2718, K.2719, D.2721, D.2723, D.2725, D.2731, E.2732 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:W.2718, A:D.2721, A:D.2723, A:D.2725, A:D.2731, A:E.2732 CA.73: 6 residues within 4Å: Chain A: Y.2759, D.2762, Y.2764, D.2766, D.2772, E.2773 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.2762, A:Y.2764, A:D.2766, A:D.2772, A:E.2773 CA.74: 7 residues within 4Å: Chain A: Y.2799, V.2800, N.2802, I.2804, N.2806, D.2814, E.2815 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:Y.2799, A:V.2800, A:I.2804, A:D.2814, A:E.2815 CA.75: 6 residues within 4Å: Chain A: F.2841, D.2844, D.2846, D.2848, D.2854, E.2855 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:F.2841, A:D.2844, A:D.2846, A:D.2848, A:D.2854 CA.76: 7 residues within 4Å: Chain A: W.2883, F.2884, D.2886, E.2888, 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.77: 6 residues within 4Å: Chain A: W.2925, D.2928, D.2930, D.2932, D.2938, E.2939 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.2925, A:D.2928, A:D.2930, A:D.2932, A:D.2938 CA.78: 7 residues within 4Å: Chain A: W.2972, V.2973, D.2975, D.2977, D.2979, D.2985, E.2986 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:V.2973, A:D.2975, A:D.2979, A:D.2985, A:E.2986 CA.79: 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:F.3012, A:D.3015, A:R.3017, A:D.3019, A:D.3025 CA.80: 6 residues within 4Å: Chain A: Y.3051, D.3054, D.3056, D.3058, D.3064, E.3065 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:Y.3051, A:D.3054, A:D.3058, A:D.3064, A:D.3064 CA.81: 7 residues within 4Å: Chain A: T.3094, V.3095, N.3097, V.3099, D.3101, D.3107, E.3108 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.3094, A:V.3099, A:D.3101, A:D.3107, A:E.3108 CA.82: 7 residues within 4Å: Chain A: W.3532, K.3533, D.3535, Q.3537, D.3539, D.3545, E.3546 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.3535, A:Q.3537, A:D.3539, A:D.3545, A:E.3546 CA.83: 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:D.3616, A:V.3618, A:D.3620, A:D.3626, A:E.3627 CA.84: 5 residues within 4Å: Chain A: W.3654, D.3657, D.3659, D.3661, D.3667 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.3654, A:D.3657, A:D.3659, A:D.3661, A:D.3667 CA.85: 7 residues within 4Å: Chain A: A.3699, V.3700, 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.86: 6 residues within 4Å: Chain A: W.3739, D.3742, I.3744, D.3746, D.3752, E.3753 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:W.3739, A:D.3742, A:I.3744, A:D.3746, A:D.3752, A:E.3753 CA.87: 6 residues within 4Å: Chain A: W.3778, D.3781, E.3783, D.3785, D.3791, E.3792 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:W.3778, A:D.3781, A:E.3783, A:D.3785, A:D.3791, A:E.3792 CA.88: 7 residues within 4Å: Chain A: L.3817, A.3818, D.3820, R.3822, D.3824, D.3830, E.3831 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.3820, A:R.3822, A:D.3824, A:D.3830, A:E.3831 CA.89: 6 residues within 4Å: Chain A: W.3861, D.3864, E.3866, D.3868, D.3874, E.3875 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.3861, A:D.3864, A:D.3868, A:D.3874, A:E.3875 CA.90: 6 residues within 4Å: Chain A: Q.3903, N.3906, V.3908, D.3910, D.3916, E.3917 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:Q.3903, A:D.3910, A:D.3916, A:D.3916, A:E.3917 CA.91: 6 residues within 4Å: Chain A: Y.3947, D.3950, V.3952, D.3954, D.3960, E.3961 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:Y.3947, A:D.3950, A:V.3952, A:D.3954, A:D.3960, A:E.3961 CA.92: 7 residues within 4Å: Chain A: W.45, D.48, T.50, D.52, D.58, E.59, R.367 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.45, A:D.48, A:T.50, A:D.52, A:D.58 CA.93: 7 residues within 4Å: Chain A: D.1391, V.1392, E.1394, N.1407, M.1408, G.1410, S.1411 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.1391, A:D.1391, A:V.1392, A:E.1394, A:M.1408 CA.94: 6 residues within 4Å: Chain A: G.3110, I.3113, E.3115, D.3130, T.3131, S.3134 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:I.3113, A:E.3115, A:D.3130, A:T.3131, A:S.3134 CA.95: 7 residues within 4Å: Chain A: D.3154, I.3155, E.3157, N.3171, V.3172, G.3174, S.3175 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.3154, A:I.3155, A:E.3157, A:E.3157, A:V.3172 CA.96: 6 residues within 4Å: Chain A: D.4009, I.4010, E.4012, N.4025, S.4026, S.4029 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.4009, A:I.4010, A:E.4012, A:S.4026, A:S.4029 CA.97: 4 residues within 4Å: Chain A: N.206, S.575, D.578, P.601 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.575, A:D.578, A:P.601 CA.98: 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.99: 4 residues within 4Å: Chain A: D.2254, D.2257, P.2279 Chain B: E.2232 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Metal complexes: A:D.2254, A:D.2257, A:D.2257, A:P.2279, B:E.2232 CA.100: 3 residues within 4Å: Chain A: R.3009, D.3344, E.3367 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.3344, A:E.3367, A:E.3367 CA.162: 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.163: 7 residues within 4Å: Chain B: W.85, V.86, D.88, D.90, D.92, D.98, E.99 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:V.86, B:D.88, B:D.92, B:D.98, B:E.99 CA.164: 6 residues within 4Å: Chain B: Y.125, D.128, V.130, D.132, D.138, E.139 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:Y.125, B:D.128, B:V.130, B:D.132, B:D.138, B:E.139 CA.165: 7 residues within 4Å: Chain B: Q.162, K.163, D.165, K.167, D.169, D.175, E.176 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:Q.162, B:D.165, B:K.167, B:D.169, B:D.175, B:E.176 CA.166: 6 residues within 4Å: Chain B: Y.200, 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.167: 7 residues within 4Å: Chain B: W.239, D.242, D.244, D.246, D.252, E.253, K.554 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.168: 7 residues within 4Å: Chain B: K.283, D.286, G.287, V.288, D.290, D.296, E.297 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:K.283, B:D.286, B:V.288, B:D.296, B:E.297 CA.169: 7 residues within 4Å: Chain B: F.1042, D.1045, V.1047, D.1048, D.1049, D.1055, E.1056 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.1045, B:V.1047, B:D.1049, B:D.1055, B:E.1056 CA.170: 7 residues within 4Å: Chain B: W.1084, D.1087, Q.1089, N.1090, D.1091, D.1097, E.1098 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.1084, B:D.1087, B:D.1091, B:D.1097, B:E.1098 CA.171: 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:D.1130, B:D.1130, B:D.1132, B:D.1134, B:E.1141 CA.172: 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.173: 6 residues within 4Å: Chain B: Y.1206, D.1209, V.1211, D.1213, D.1219, E.1220 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:Y.1206, B:D.1209, B:V.1211, B:D.1213, B:D.1219 CA.174: 7 residues within 4Å: Chain B: W.1249, E.1250, D.1252, H.1254, D.1256, D.1262, E.1263 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.1252, B:H.1254, B:D.1256, B:D.1262, B:E.1263 CA.175: 6 residues within 4Å: Chain B: W.1289, 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.176: 6 residues within 4Å: Chain B: A.1331, D.1334, V.1336, D.1338, D.1344, E.1345 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:A.1331, B:V.1336, B:D.1338, B:D.1344, B:E.1345 CA.177: 7 residues within 4Å: Chain B: W.2718, K.2719, 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.178: 6 residues within 4Å: Chain B: Y.2759, D.2762, Y.2764, D.2766, D.2772, E.2773 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.2762, B:Y.2764, B:D.2766, B:D.2772, B:E.2773 CA.179: 7 residues within 4Å: Chain B: Y.2799, V.2800, N.2802, I.2804, N.2806, D.2814, E.2815 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:Y.2799, B:V.2800, B:I.2804, B:D.2814, B:E.2815 CA.180: 6 residues within 4Å: Chain B: F.2841, D.2844, D.2846, D.2848, D.2854, E.2855 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:F.2841, B:D.2844, B:D.2846, B:D.2848, B:D.2854 CA.181: 7 residues within 4Å: Chain B: W.2883, F.2884, D.2886, E.2888, D.2890, D.2896, E.2897 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.2886, B:E.2888, B:D.2890, B:D.2896, B:E.2897 CA.182: 6 residues within 4Å: Chain B: W.2925, D.2928, 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.2932, B:D.2938 CA.183: 7 residues within 4Å: Chain B: W.2972, V.2973, D.2975, D.2977, D.2979, D.2985, E.2986 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:V.2973, B:D.2975, B:D.2979, B:D.2985, B:E.2986 CA.184: 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:R.3017, B:D.3019, B:D.3025 CA.185: 6 residues within 4Å: Chain B: Y.3051, D.3054, D.3056, D.3058, D.3064, E.3065 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:Y.3051, B:D.3054, B:D.3058, B:D.3064, B:D.3064 CA.186: 7 residues within 4Å: Chain B: T.3094, V.3095, N.3097, V.3099, D.3101, D.3107, E.3108 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.3094, B:V.3099, B:D.3101, B:D.3107, B:E.3108 CA.187: 7 residues within 4Å: Chain B: W.3532, K.3533, 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.188: 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:D.3616, B:V.3618, B:D.3620, B:D.3626, B:E.3627 CA.189: 5 residues within 4Å: Chain B: W.3654, D.3657, D.3659, D.3661, D.3667 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.3654, B:D.3657, B:D.3659, B:D.3661, B:D.3667 CA.190: 7 residues within 4Å: Chain B: A.3699, V.3700, 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.191: 6 residues within 4Å: Chain B: W.3739, D.3742, I.3744, D.3746, D.3752, E.3753 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:W.3739, B:D.3742, B:I.3744, B:D.3746, B:D.3752, B:E.3753 CA.192: 6 residues within 4Å: Chain B: W.3778, D.3781, E.3783, D.3785, D.3791, E.3792 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:W.3778, B:D.3781, B:E.3783, B:D.3785, B:D.3791, B:E.3792 CA.193: 7 residues within 4Å: Chain B: L.3817, A.3818, D.3820, R.3822, D.3824, D.3830, E.3831 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.3820, B:R.3822, B:D.3824, B:D.3830, B:E.3831 CA.194: 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:D.3868, B:D.3874, B:E.3875 CA.195: 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:D.3910, B:D.3916, B:D.3916, B:E.3917 CA.196: 6 residues within 4Å: Chain B: Y.3947, D.3950, V.3952, D.3954, D.3960, E.3961 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:Y.3947, B:D.3950, B:V.3952, B:D.3954, B:D.3960, B:E.3961 CA.197: 7 residues within 4Å: Chain B: W.45, D.48, T.50, D.52, D.58, E.59, R.367 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.198: 7 residues within 4Å: Chain B: D.1391, V.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:D.1391, B:V.1392, B:E.1394, B:M.1408 CA.199: 6 residues within 4Å: Chain B: G.3110, I.3113, E.3115, D.3130, T.3131, S.3134 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:I.3113, B:E.3115, B:D.3130, B:T.3131, B:S.3134 CA.200: 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.201: 6 residues within 4Å: Chain B: D.4009, I.4010, E.4012, N.4025, S.4026, S.4029 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.4009, B:I.4010, B:E.4012, B:S.4026, B:S.4029 CA.202: 4 residues within 4Å: Chain B: N.206, S.575, D.578, P.601 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.575, B:D.578, B:P.601 CA.203: 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.204: 4 residues within 4Å: Chain A: E.2232 Chain B: D.2254, D.2257, P.2279 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Metal complexes: B:D.2254, B:D.2257, B:D.2257, B:P.2279, A:E.2232 CA.205: 3 residues within 4Å: Chain B: R.3009, D.3344, E.3367 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.3344, B:E.3367, B:E.3367

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beenken, A. et al., Structures of LRP2 reveal a molecular machine for endocytosis. Cell (2023)

Release Date

2023-02-08

Peptides

Low-density lipoprotein receptor-related protein 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Low-density lipoprotein receptor-related protein 2

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