SMTL ID : 8jxi.1

rat megalin RAP complex wingB

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: 6 residues within 4Å: Chain B: M.426, R.512, W.528, W.557, W.618, D.1132 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.2: 7 residues within 4Å: Chain B: F.741, R.828, W.844, W.870, N.872, H.914, W.930 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.741, B:W.844 Hydrogen bonds: B:R.828, B:R.828, B:N.872, B:N.872

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.3: 3 residues within 4Å: Chain B: K.446, E.459, N.462 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: F.1062, N.1063 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.4: 5 residues within 4Å: Chain B: D.388, S.389, F.390, A.652, 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.5: 3 residues within 4Å: Chain B: K.849, N.865, H.1254 No protein-ligand interaction detected (PLIP)

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

NAG.7: 2 residues within 4Å: Chain B: N.338, N.340 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.338, B:N.338, B:N.340 NAG.8: 2 residues within 4Å: Chain B: N.1187, C.1188 No protein-ligand interaction detected (PLIP) NAG.29: 1 residues within 4Å: Chain C: N.2782 No protein-ligand interaction detected (PLIP) NAG.30: 1 residues within 4Å: Chain C: N.2810 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.2810

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

A2G.9: 3 residues within 4Å: Chain B: T.221, C.222, G.223 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.221 A2G.10: 6 residues within 4Å: Chain B: N.780, R.781, Y.1001, T.1022, Q.1023, Q.1024 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.781 A2G.11: 3 residues within 4Å: Chain B: N.1063, N.1064, T.1065 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.1065, B:T.1065, B:T.1065 A2G.12: 2 residues within 4Å: Chain B: S.1107, T.1109 No protein-ligand interaction detected (PLIP) A2G.13: 3 residues within 4Å: Chain B: S.1147, T.1149, C.1150 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.1149 A2G.14: 1 residues within 4Å: Chain B: T.1225 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.1225 A2G.15: 2 residues within 4Å: Chain B: P.1269, T.1271 No protein-ligand interaction detected (PLIP) A2G.16: 3 residues within 4Å: Chain B: T.1103, A.1105, T.1106 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.1105 Hydrogen bonds: B:A.1105, B:T.1106 A2G.31: 3 residues within 4Å: Chain B: Q.1009 Chain C: H.2740, T.2741 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:H.2740, C:T.2741, C:T.2741, B:Q.1009

16 x CA: CALCIUM ION(Non-covalent)

CA.17: 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:Y.200, B:D.203, B:D.205, B:D.207, B:D.213 CA.18: 7 residues within 4Å: Chain B: W.239, C.241, 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.242, B:D.244, B:D.252, B:E.253 CA.19: 8 residues within 4Å: Chain B: K.283, V.284, C.285, D.286, 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:D.290, B:D.296, B:E.297 CA.20: 4 residues within 4Å: Chain B: S.575, D.578, P.601, T.1131 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.575, B:D.578, B:P.601, B:T.1131 CA.21: 3 residues within 4Å: Chain B: A.888, D.891, T.913 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:A.888, B:D.891, B:T.913 CA.22: 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:V.1047, B:D.1049, B:D.1055, B:E.1056 CA.23: 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:Q.1089, B:D.1091, B:D.1097, B:E.1098 CA.24: 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.25: 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.1170, B:D.1172, B:D.1174, B:D.1180 CA.26: 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:V.1211, B:D.1213, B:D.1219, B:E.1220 CA.27: 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.1262, B:E.1263 CA.28: 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.32: 6 residues within 4Å: Chain C: W.2718, D.2721, D.2723, D.2725, D.2731, E.2732 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:W.2718, C:D.2721, C:D.2723, C:D.2725, C:D.2731 CA.33: 6 residues within 4Å: Chain C: Y.2759, D.2762, Y.2764, D.2766, D.2772, E.2773 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:Y.2759, C:D.2762, C:Y.2764, C:D.2766, C:D.2772 CA.34: 8 residues within 4Å: Chain C: Y.2799, V.2800, C.2801, N.2802, I.2804, N.2806, D.2814, E.2815 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:Y.2799, C:I.2804, C:D.2814, C:E.2815, C:E.2815 CA.35: 6 residues within 4Å: Chain C: F.2841, D.2844, D.2846, D.2848, D.2854, E.2855 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:F.2841, C:D.2844, C:D.2846, C:D.2848, C:D.2854

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

Alpha-2-macroglobulin receptor-associated protein

LDL receptor related protein 2

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