SMTL ID : 9j3p.1

Human Pigment Epithelium-Derived Factor with Zinc Ions Crystallized in P2(1)2(1)2(1) Space Group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-pentamer

Ligands

7 x ZN: ZINC ION(Non-covalent)

ZN.1: 1 residues within 4Å: Chain A: H.361 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.361, H2O.4 ZN.10: 6 residues within 4Å: Chain B: E.216 Chain C: D.24, P.25, F.26, H.279, R.283 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Metal complexes: C:D.24, C:D.24, C:H.279, B:E.216, B:E.216 ZN.11: 1 residues within 4Å: Chain C: H.361 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.361 ZN.15: 3 residues within 4Å: Chain B: H.361 Chain D: A.360, H.361 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Metal complexes: B:H.361, D:H.361 ZN.19: 5 residues within 4Å: Chain E: D.24, P.25, F.26, H.279, R.283 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.24, E:D.24, E:H.279, H2O.24 ZN.20: 1 residues within 4Å: Chain E: H.361 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.361, H2O.25 ZN.21: 1 residues within 4Å: Chain E: H.85 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.85, H2O.25, H2O.26

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: Q.158, N.161, R.174 5 PLIP interactions: 5 interactions with chain A Water bridges: A:N.161, A:R.174, A:R.174, A:R.174 Salt bridges: A:R.174 SO4.5: 4 residues within 4Å: Chain B: T.144, R.145, W.163, Q.167 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.144, B:R.145, B:W.163, B:Q.167 Water bridges: B:R.121 Salt bridges: B:R.145 SO4.6: 5 residues within 4Å: Chain A: K.313 Chain B: D.44, R.47, V.48, M.312 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.44, B:D.44, B:V.48 Salt bridges: B:R.47, A:K.313 Water bridges: A:K.313 SO4.12: 6 residues within 4Å: Chain C: G.143, T.144, R.145, W.163, Q.167 Chain E: R.129 7 PLIP interactions: 1 interactions with chain E, 6 interactions with chain C Salt bridges: E:R.129, C:R.145 Hydrogen bonds: C:T.144, C:T.144, C:R.145, C:W.163, C:Q.167 SO4.13: 3 residues within 4Å: Chain C: Q.158, N.161, R.174 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.158 Salt bridges: C:R.174 SO4.14: 3 residues within 4Å: Chain C: K.131, S.132, S.133 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.132, C:S.133 Salt bridges: C:K.131 SO4.16: 4 residues within 4Å: Chain D: T.144, R.145, W.163, Q.167 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.145, D:W.163, D:Q.167 Water bridges: D:R.121 Salt bridges: D:R.145 SO4.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.22: 5 residues within 4Å: Chain C: P.112 Chain E: R.121, R.145, W.163, Q.167 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:W.163, E:Q.167

7 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.3: 6 residues within 4Å: Chain A: D.44, R.47, V.48, E.311, M.312 Chain B: K.313 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.313 PG0.4: 7 residues within 4Å: Chain A: D.97, H.99, G.100, K.103, E.104, K.140, S.141 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.97, A:K.140 PG0.7: 6 residues within 4Å: Chain B: K.296, L.297, K.298, E.343, W.344, N.345 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.296, B:E.343, B:N.345 PG0.8: 9 residues within 4Å: Chain B: N.57, V.58, L.59, L.299, S.300, Y.301, G.397, P.398 Chain E: R.154 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.57, B:P.398 Water bridges: B:L.59 PG0.9: 5 residues within 4Å: Chain B: T.110, L.116, K.117, G.143, Q.167 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.116, B:K.117 PG0.18: 1 residues within 4Å: Chain D: R.129 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.129 PG0.23: 6 residues within 4Å: Chain E: N.57, K.298, L.299, S.300, G.397, P.398 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.57, E:P.398, E:P.398

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chistyakov, D.V. et al., Zinc-mediated mechanism of neurodegeneration in glaucoma: a role of pigment epithelium-derived factor. To Be Published

Release Date

2025-06-18

Peptides

Pigment epithelium-derived factor: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Pigment epithelium-derived factor

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