SMTL ID : 8jxh.1

rat megalin RAP complex wingA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-mer

Ligands

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

UNK-UNK-UNK-UNK-UNK-UNK.1: 3 residues within 4Å: Chain C: M.426, R.512, W.618 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.512, C:R.512 UNK-UNK-UNK-UNK-UNK-UNK.2: 7 residues within 4Å: Chain C: E.786, R.828, W.844, W.870, N.872, H.914, W.930 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.844, C:W.870 Hydrogen bonds: C:R.828, C:R.828, C:N.872, C:N.872

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

NAG-NAG.3: 2 residues within 4Å: Chain C: E.459, N.462 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: Q.1058, F.1062, N.1063, N.1064 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1063

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.4: 3 residues within 4Å: Chain C: P.862, N.865, H.1254 No protein-ligand interaction detected (PLIP)

1 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.6: 5 residues within 4Å: Chain C: D.388, S.389, F.390, Q.433, N.657 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.389

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

NAG.7: 1 residues within 4Å: Chain B: N.2782 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain B: N.2810, D.2811 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.2810, B:D.2811 NAG.14: 3 residues within 4Å: Chain C: N.338, N.340, I.346 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.338 NAG.15: 2 residues within 4Å: Chain C: L.1186, N.1187 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1187

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

A2G.9: 3 residues within 4Å: Chain B: T.2741, C.2742 Chain C: Q.1009 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.2741 A2G.16: 2 residues within 4Å: Chain C: T.221, T.679 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.221, C:T.221 A2G.17: 4 residues within 4Å: Chain C: N.780, R.781, Y.1001, T.1022 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.781, C:T.1022 A2G.18: 2 residues within 4Å: Chain C: T.1065, C.1066 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.1065 Hydrogen bonds: C:C.1066, C:C.1066 A2G.19: 2 residues within 4Å: Chain C: S.1108, T.1109 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.1109 A2G.20: 2 residues within 4Å: Chain C: G.1148, T.1149 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.1149 A2G.21: 2 residues within 4Å: Chain C: T.1225, P.1227 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.1225, C:T.1225 A2G.22: 3 residues within 4Å: Chain C: T.1271, C.1272, S.1273 No protein-ligand interaction detected (PLIP) A2G.23: 3 residues within 4Å: Chain C: T.1103, A.1105, T.1106 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.1103

16 x CA: CALCIUM ION(Non-covalent)

CA.10: 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.11: 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.12: 7 residues within 4Å: Chain B: Y.2799, C.2801, 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.13: 7 residues within 4Å: Chain B: F.2841, L.2842, C.2843, D.2844, D.2846, 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.2854, B:E.2855 CA.24: 6 residues within 4Å: Chain C: Y.200, D.203, D.205, D.207, D.213, E.214 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.203, C:D.205, C:D.207, C:D.213, C:E.214 CA.25: 7 residues within 4Å: Chain C: W.239, C.241, D.242, D.244, D.246, D.252, E.253 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:W.239, C:D.242, C:D.244, C:D.246, C:D.252 CA.26: 8 residues within 4Å: Chain C: K.283, V.284, C.285, D.286, V.288, D.290, D.296, E.297 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.286, C:V.288, C:D.290, C:D.296, C:E.297 CA.27: 5 residues within 4Å: Chain C: S.575, D.578, P.601, T.1131, D.1132 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:S.575, C:D.578, C:D.578, C:P.601, C:T.1131 CA.28: 4 residues within 4Å: Chain C: A.888, F.889, D.891, T.913 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:A.888, C:D.891, C:T.913 CA.29: 6 residues within 4Å: Chain C: F.1042, D.1045, V.1047, D.1049, D.1055, E.1056 6 PLIP interactions: 6 interactions with chain C Metal complexes: C:F.1042, C:D.1045, C:V.1047, C:D.1049, C:D.1055, C:E.1056 CA.30: 6 residues within 4Å: Chain C: W.1084, D.1087, Q.1089, D.1091, D.1097, E.1098 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:W.1084, C:D.1087, C:D.1091, C:D.1097, C:E.1098 CA.31: 6 residues within 4Å: Chain C: W.1127, D.1130, D.1132, D.1134, D.1140, E.1141 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:W.1127, C:D.1130, C:D.1132, C:D.1134, C:D.1140 CA.32: 6 residues within 4Å: Chain C: Y.1167, D.1170, D.1172, D.1174, D.1180, E.1181 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:Y.1167, C:D.1170, C:D.1172, C:D.1174, C:E.1181 CA.33: 6 residues within 4Å: Chain C: Y.1206, D.1209, V.1211, D.1213, D.1219, E.1220 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:Y.1206, C:V.1211, C:D.1213, C:D.1219, C:E.1220 CA.34: 6 residues within 4Å: Chain C: W.1249, D.1252, H.1254, D.1256, D.1262, E.1263 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:W.1249, C:D.1252, C:H.1254, C:D.1256, C:D.1262 CA.35: 6 residues within 4Å: Chain C: W.1289, D.1292, D.1294, D.1296, D.1302, E.1303 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:W.1289, C:D.1292, C:D.1294, C:D.1296, C:E.1303

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

Alpha-2-macroglobulin receptor-associated protein: A
LDL receptor related protein 2: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
B

Alpha-2-macroglobulin receptor-associated protein

LDL receptor related protein 2

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