SMTL ID : 5jgf.1

Crystal structure of mApe1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-12-mer

Ligands

24 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.91, D.262, D.263, E.298, D.344 Ligands: ZN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.91, A:D.262, A:D.344, H2O.3, H2O.10 ZN.2: 4 residues within 4Å: Chain A: D.262, E.299, H.438 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.262, A:E.299, A:E.299, A:H.438, H2O.3 ZN.3: 5 residues within 4Å: Chain B: D.262, E.298, E.299, H.438 Ligands: ZN.4 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.262, B:E.299, B:H.438, H2O.4, H2O.25 ZN.4: 7 residues within 4Å: Chain B: H.91, D.262, D.263, E.298, E.299, D.344 Ligands: ZN.3 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.91, B:D.262, B:D.344, H2O.25, H2O.31 ZN.5: 7 residues within 4Å: Chain C: H.91, D.262, D.263, E.298, E.299, D.344 Ligands: ZN.6 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.91, C:D.262, C:D.344, H2O.47, H2O.55 ZN.6: 4 residues within 4Å: Chain C: D.262, E.299, H.438 Ligands: ZN.5 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.262, C:E.299, C:E.299, C:H.438, H2O.47 ZN.7: 6 residues within 4Å: Chain D: H.91, D.262, D.263, E.298, D.344 Ligands: ZN.8 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.91, D:D.262, D:D.344, H2O.70, H2O.78 ZN.8: 4 residues within 4Å: Chain D: D.262, E.299, H.438 Ligands: ZN.7 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.262, D:E.299, D:H.438, H2O.50, H2O.70 ZN.9: 6 residues within 4Å: Chain E: H.91, D.262, D.263, E.298, D.344 Ligands: ZN.10 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.91, E:D.262, E:D.344, H2O.95, H2O.102 ZN.10: 4 residues within 4Å: Chain E: D.262, E.299, H.438 Ligands: ZN.9 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.262, E:E.299, E:H.438, H2O.95, H2O.124 ZN.11: 5 residues within 4Å: Chain F: D.262, E.298, E.299, H.438 Ligands: ZN.12 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.262, F:E.299, F:H.438, H2O.96, H2O.118 ZN.12: 7 residues within 4Å: Chain F: H.91, D.262, D.263, E.298, E.299, D.344 Ligands: ZN.11 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.91, F:D.262, F:D.344, H2O.118, H2O.124 ZN.13: 7 residues within 4Å: Chain G: H.91, D.262, D.263, E.298, E.299, D.344 Ligands: ZN.14 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:H.91, G:D.262, G:D.344, H2O.140, H2O.147 ZN.14: 4 residues within 4Å: Chain G: D.262, E.299, H.438 Ligands: ZN.13 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.262, G:E.299, G:E.299, G:H.438, H2O.140 ZN.15: 6 residues within 4Å: Chain H: H.91, D.262, D.263, E.298, D.344 Ligands: ZN.16 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:H.91, H:D.262, H:D.344, H2O.162, H2O.171 ZN.16: 4 residues within 4Å: Chain H: D.262, E.299, H.438 Ligands: ZN.15 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.262, H:E.299, H:H.438, H2O.143, H2O.162 ZN.17: 6 residues within 4Å: Chain I: H.91, D.262, D.263, E.298, D.344 Ligands: ZN.18 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:H.91, I:D.262, I:D.344, H2O.187, H2O.195 ZN.18: 4 residues within 4Å: Chain I: D.262, E.299, H.438 Ligands: ZN.17 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:D.262, I:E.299, I:E.299, I:H.438, H2O.187 ZN.19: 5 residues within 4Å: Chain J: D.262, E.298, E.299, H.438 Ligands: ZN.20 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:D.262, J:E.299, J:H.438, H2O.189, H2O.210 ZN.20: 7 residues within 4Å: Chain J: H.91, D.262, D.263, E.298, E.299, D.344 Ligands: ZN.19 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:H.91, J:D.262, J:D.344, H2O.210, H2O.216 ZN.21: 7 residues within 4Å: Chain K: H.91, D.262, D.263, E.298, E.299, D.344 Ligands: ZN.22 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:H.91, K:D.262, K:D.344, H2O.232, H2O.240 ZN.22: 4 residues within 4Å: Chain K: D.262, E.299, H.438 Ligands: ZN.21 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:D.262, K:E.299, K:E.299, K:H.438, H2O.232 ZN.23: 6 residues within 4Å: Chain L: H.91, D.262, D.263, E.298, D.344 Ligands: ZN.24 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:H.91, L:D.262, L:D.344, H2O.255, H2O.263 ZN.24: 4 residues within 4Å: Chain L: D.262, E.299, H.438 Ligands: ZN.23 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:D.262, L:E.299, L:H.438, H2O.235, H2O.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamasaki, A. et al., Structural Basis for Receptor-Mediated Selective Autophagy of Aminopeptidase I Aggregates. Cell Rep (2016)

Release Date

2016-06-29

Peptides

Vacuolar aminopeptidase 1: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

Vacuolar aminopeptidase 1