SMTL ID : 8jxc.1

rat megalin wingB

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

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

UNK-UNK-UNK-UNK-UNK-UNK.1: 5 residues within 4Å: Chain A: M.443, E.469, R.512, W.557, W.618 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: 9 residues within 4Å: Chain A: F.741, E.786, R.828, W.844, W.870, N.872, A.888, H.914, W.930 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.870 Hydrogen bonds: A:R.828, A:R.828, A:N.872, A: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 A: F.390, A.652, L.653, N.657 No protein-ligand interaction detected (PLIP)

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.4: 4 residues within 4Å: Chain A: P.862, I.863, N.865, H.1254 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: Q.1058, F.1062, N.1063 No protein-ligand interaction detected (PLIP)

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

NAG.6: 2 residues within 4Å: Chain A: S.339, N.340 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.340 NAG.7: 2 residues within 4Å: Chain A: E.459, N.462 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.462 NAG.8: 3 residues within 4Å: Chain A: N.1187, C.1188, T.1189 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.1189 NAG.33: 2 residues within 4Å: Chain A: N.2782, T.2784 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.2782, A:T.2784 NAG.34: 2 residues within 4Å: Chain A: N.2810, D.2811 No protein-ligand interaction detected (PLIP)

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

A2G.9: 3 residues within 4Å: Chain A: T.221, C.222, G.223 No protein-ligand interaction detected (PLIP) A2G.10: 5 residues within 4Å: Chain A: N.780, R.781, Y.1001, T.1022, Q.1023 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.780, A:T.1022 A2G.11: 4 residues within 4Å: Chain A: R.1043, T.1065, C.1066, S.1067 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.1043, A:T.1065 A2G.12: 3 residues within 4Å: Chain A: S.1107, S.1108, T.1109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.1109 A2G.13: 1 residues within 4Å: Chain A: T.1149 No protein-ligand interaction detected (PLIP) A2G.14: 3 residues within 4Å: Chain A: T.1225, R.1226, P.1228 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.1228 A2G.15: 4 residues within 4Å: Chain A: T.1271, C.1272, S.1273, C.1284 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.1271 A2G.35: 3 residues within 4Å: Chain A: Q.1009, T.2741, C.2742 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.2741

17 x CA: CALCIUM ION(Non-covalent)

CA.16: 7 residues within 4Å: Chain A: Y.200, C.202, 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.17: 6 residues within 4Å: Chain A: W.239, D.242, D.244, D.246, D.252, E.253 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.18: 8 residues within 4Å: Chain A: K.283, C.285, D.286, G.287, V.288, D.290, D.296, E.297 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.286, A:V.288, A:D.290, A:D.296, A:E.297 CA.19: 4 residues within 4Å: Chain A: S.575, D.578, P.601, T.1131 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:S.575, A:D.578, A:D.578, A:P.601, A:T.1131 CA.20: 3 residues within 4Å: Chain A: A.888, D.891, T.913 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:A.888, A:D.891, A:T.913 CA.21: 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:D.1055 CA.22: 7 residues within 4Å: Chain A: W.1084, C.1086, D.1087, Q.1089, 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.23: 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.24: 7 residues within 4Å: Chain A: Y.1167, C.1169, 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:D.1180 CA.25: 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.26: 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:H.1254, A:D.1256, A:D.1262, A:E.1263 CA.27: 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:D.1292, A:D.1294, A:D.1296, A:D.1302, A:E.1303 CA.28: 6 residues within 4Å: Chain A: W.2718, C.2720, D.2721, D.2723, D.2725, D.2731 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.2718, A:D.2721, A:D.2723, A:D.2725, A:D.2731 CA.29: 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:Y.2759, A:D.2762, A:Y.2764, A:D.2766, A:D.2772 CA.30: 7 residues within 4Å: Chain A: Y.2799, 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.31: 7 residues within 4Å: Chain A: F.2841, C.2843, 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.32: 8 residues within 4Å: Chain A: W.2883, C.2885, D.2886, G.2887, 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.2896, A:E.2897

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LDL receptor related protein 2

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