SMTL ID : 8jxb.1

Cryo-EM structure of rat megalin wingAc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

UNK-UNK-UNK-UNK-UNK-UNK.1: 4 residues within 4Å: Chain B: M.426, R.512, H.602, W.618 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.512, B:R.512 UNK-UNK-UNK-UNK-UNK-UNK.2: 7 residues within 4Å: Chain B: F.741, R.828, W.844, W.870, N.872, H.914, W.930 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.844 Hydrogen bonds: B:R.828, B:R.828, B:N.872

1 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.3: 4 residues within 4Å: Chain B: S.389, F.390, Q.433, N.657 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.389

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.4: 2 residues within 4Å: Chain B: N.865, H.1254 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: V.1061, N.1063 No protein-ligand interaction detected (PLIP)

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

NAG.6: 3 residues within 4Å: Chain A: N.2782, T.2784, T.2785 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.2782, A:T.2785 NAG.7: 1 residues within 4Å: Chain A: N.2810 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.2810 NAG.15: 3 residues within 4Å: Chain B: N.338, N.340, I.346 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.346 Hydrogen bonds: B:N.340 NAG.16: 2 residues within 4Å: Chain B: E.459, N.462 No protein-ligand interaction detected (PLIP) NAG.17: 2 residues within 4Å: Chain B: V.1185, N.1187 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.1185

8 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Post Translational Modification)(Non-covalent)

A2G.8: 2 residues within 4Å: Chain A: T.2741 Chain B: Q.1009 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.1009, A:T.2741 A2G.18: 5 residues within 4Å: Chain B: D.220, T.221, C.222, G.223, T.679 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.222 A2G.19: 6 residues within 4Å: Chain B: N.780, R.781, Y.1001, T.1022, Q.1023, Q.1024 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.780, B:R.781, B:T.1022 A2G.20: 3 residues within 4Å: Chain B: N.1063, N.1064, T.1065 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.1065 A2G.21: 3 residues within 4Å: Chain B: T.1109, C.1110, P.1111 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.1109 Hydrogen bonds: B:T.1109 A2G.22: 4 residues within 4Å: Chain B: T.1149, C.1150, Q.1151, P.1152 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.1150, B:C.1150 A2G.23: 2 residues within 4Å: Chain B: T.1225, R.1226 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.1225 A2G.24: 3 residues within 4Å: Chain B: T.1271, C.1272, S.1273 No protein-ligand interaction detected (PLIP)

18 x CA: CALCIUM ION(Non-covalent)

CA.9: 7 residues within 4Å: Chain A: W.2718, C.2720, D.2721, D.2723, D.2725, D.2731, E.2732 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.2721, A:D.2723, A:D.2725, A:D.2731, A:E.2732 CA.10: 5 residues within 4Å: Chain A: Y.2759, D.2762, Y.2764, D.2766, D.2772 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.2762, A:D.2762, A:Y.2764, A:D.2766, A:D.2772 CA.11: 8 residues within 4Å: Chain A: Y.2799, V.2800, C.2801, N.2802, I.2804, N.2806, D.2814, E.2815 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:Y.2799, A:I.2804, A:D.2814, A:D.2814, A:E.2815 CA.12: 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:D.2844, A:D.2846, A:D.2848, A:D.2854, A:E.2855 CA.13: 7 residues within 4Å: Chain A: I.2879, W.2883, D.2886, E.2888, D.2890, D.2896, E.2897 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.2883, A:D.2886, A:E.2888, A:D.2890, A:E.2897 CA.14: 7 residues within 4Å: Chain A: W.2925, C.2927, D.2928, D.2930, D.2932, D.2938, E.2939 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.2928, A:D.2930, A:D.2932, A:D.2938, A:E.2939 CA.25: 7 residues within 4Å: Chain B: Y.200, 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.26: 8 residues within 4Å: Chain B: W.239, C.241, D.242, G.243, D.244, D.246, D.252, E.253 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.239, B:D.242, B:D.244, B:D.252, B:E.253 CA.27: 7 residues within 4Å: Chain B: K.283, V.284, C.285, D.286, V.288, D.296, E.297 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:K.283, B:D.286, B:D.296, B:D.296, B:E.297 CA.28: 5 residues within 4Å: Chain B: S.575, D.578, P.601, T.1131, D.1132 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:S.575, B:D.578, B:D.578, B:P.601, B:T.1131 CA.29: 3 residues within 4Å: Chain B: A.888, D.891, T.913 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:A.888, B:D.891, B:D.891, B:T.913 CA.30: 6 residues within 4Å: Chain B: F.1042, D.1045, V.1047, D.1049, D.1055, E.1056 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:F.1042, B:D.1045, B:V.1047, B:D.1055, B:E.1056 CA.31: 7 residues within 4Å: Chain B: R.422, 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.1091, B:E.1098 CA.32: 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.1132, B:D.1134, B:D.1140 CA.33: 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.34: 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.1219, B:E.1220 CA.35: 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:H.1254, B:D.1256, B:D.1262, B:E.1263 CA.36: 8 residues within 4Å: Chain B: W.1289, I.1290, C.1291, D.1292, D.1294, D.1296, D.1302, E.1303 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:W.1289, B:D.1292, B:D.1296, B:D.1302

Links

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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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

LDL receptor related protein 2

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