SMTL ID : 9j3q.1

Human Pigment Epithelium-Derived Factor with Zinc Ion Crystallized in P22(1)2(1) Space Group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.24, P.25, F.26, H.279, R.283 Ligands: PG0.37 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.24, A:D.24, A:H.279, H2O.5

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

PG0.2: 10 residues within 4Å: Chain A: S.82, H.85, R.86, Y.90, D.91, I.93, S.94, S.95 Ligands: PG0.5, PG0.9 Ligand excluded by PLIP PG0.3: 7 residues within 4Å: Chain A: E.125, S.184, K.329, P.330, I.331, K.332, T.334 Ligand excluded by PLIP PG0.4: 7 residues within 4Å: Chain A: T.306, Q.310, Q.315, F.318, L.333, T.334 Ligands: PG0.29 Ligand excluded by PLIP PG0.5: 9 residues within 4Å: Chain A: L.74, E.81, H.85, S.95, P.96, D.97, I.98, H.99 Ligands: PG0.2 Ligand excluded by PLIP PG0.6: 10 residues within 4Å: Chain A: S.320, P.321, D.322, F.323, S.324, T.327, G.328, K.329, P.330 Ligands: PG0.16 Ligand excluded by PLIP PG0.7: 11 residues within 4Å: Chain A: D.44, R.47, V.48, R.86, Y.89, E.311, M.312, K.313 Ligands: PG0.17, PG0.18, PG0.24 Ligand excluded by PLIP PG0.8: 10 residues within 4Å: Chain A: K.205, T.206, S.207, E.209, M.223, M.224, S.225, T.293, H.369, N.371 Ligand excluded by PLIP PG0.9: 6 residues within 4Å: Chain A: R.79, S.82, I.83, R.86, D.91 Ligands: PG0.2 Ligand excluded by PLIP PG0.10: 6 residues within 4Å: Chain A: P.112, Q.113, N.115, Q.196, T.249, A.349 Ligand excluded by PLIP PG0.11: 7 residues within 4Å: Chain A: A.173, K.298, L.299, S.300, G.397, P.398 Ligands: PG0.13 Ligand excluded by PLIP PG0.12: 6 residues within 4Å: Chain A: E.104, D.107, T.108, A.111, Q.113 Ligands: PG0.23 Ligand excluded by PLIP PG0.13: 8 residues within 4Å: Chain A: G.170, K.171, L.172, A.173, H.192, K.298 Ligands: PG0.11, PG0.35 Ligand excluded by PLIP PG0.14: 3 residues within 4Å: Chain A: P.359, A.360, H.361 Ligand excluded by PLIP PG0.15: 3 residues within 4Å: Chain A: N.152, P.153, R.154 Ligand excluded by PLIP PG0.16: 9 residues within 4Å: Chain A: E.77, R.79, T.80, I.83, S.316, S.320, P.321, D.322 Ligands: PG0.6 Ligand excluded by PLIP PG0.17: 9 residues within 4Å: Chain A: G.17, D.44, R.86, A.87, Y.89, L.92, K.313 Ligands: PG0.7, PG0.18 Ligand excluded by PLIP PG0.18: 12 residues within 4Å: Chain A: N.40, Y.43, D.44, R.47, Y.89, L.273, T.274, S.275, E.276 Ligands: PG0.7, PG0.17, PG0.24 Ligand excluded by PLIP PG0.19: 5 residues within 4Å: Chain A: L.235, S.237, S.240, L.260 Ligands: PG0.20 Ligand excluded by PLIP PG0.20: 8 residues within 4Å: Chain A: K.242, L.258, P.259, L.260, H.369, N.371, Q.372 Ligands: PG0.19 Ligand excluded by PLIP PG0.21: 12 residues within 4Å: Chain A: K.103, L.106, D.107, T.110, S.118, A.119, S.141, Y.142, G.143, Q.167 Ligands: PG0.22, PG0.23 Ligand excluded by PLIP PG0.22: 14 residues within 4Å: Chain A: L.63, S.64, T.67, L.106, T.110, S.118, A.119, S.120, Y.142, G.143, T.144, W.163, Q.167 Ligands: PG0.21 Ligand excluded by PLIP PG0.23: 6 residues within 4Å: Chain A: D.107, T.110, A.111, P.112 Ligands: PG0.12, PG0.21 Ligand excluded by PLIP PG0.24: 6 residues within 4Å: Chain A: R.47, E.271, S.272, T.274 Ligands: PG0.7, PG0.18 Ligand excluded by PLIP PG0.25: 9 residues within 4Å: Chain A: L.149, G.151, N.152, P.153, D.156, I.179, P.180, D.181, I.183 Ligand excluded by PLIP PG0.26: 7 residues within 4Å: Chain A: H.99, G.100, K.103, E.104, D.107, K.140, S.141 Ligand excluded by PLIP PG0.27: 7 residues within 4Å: Chain A: V.221, P.222, K.296, L.297, K.298, P.395, R.396 Ligand excluded by PLIP PG0.28: 5 residues within 4Å: Chain A: K.177, E.302, G.303, E.304, E.337 Ligand excluded by PLIP PG0.29: 7 residues within 4Å: Chain A: E.178, I.179, P.180, E.304, T.334, Q.335 Ligands: PG0.4 Ligand excluded by PLIP PG0.30: 5 residues within 4Å: Chain A: V.230, T.287, V.288, Q.289 Ligands: PG0.31 Ligand excluded by PLIP PG0.31: 6 residues within 4Å: Chain A: V.230, L.231, R.232, P.247, T.287 Ligands: PG0.30 Ligand excluded by PLIP PG0.32: 3 residues within 4Å: Chain A: D.202, R.204, K.205 Ligand excluded by PLIP PG0.33: 5 residues within 4Å: Chain A: D.210, Y.212, T.218, V.219, R.220 Ligand excluded by PLIP PG0.34: 5 residues within 4Å: Chain A: Q.165, A.166, K.169, G.170 Ligands: PG0.35 Ligand excluded by PLIP PG0.35: 6 residues within 4Å: Chain A: Q.165, K.169, G.170, K.171 Ligands: PG0.13, PG0.34 Ligand excluded by PLIP PG0.36: 11 residues within 4Å: Chain A: T.55, T.56, N.57, L.213, R.217, Q.264, L.393, D.394, R.396, G.397, P.398 Ligand excluded by PLIP PG0.37: 6 residues within 4Å: Chain A: E.23, D.24, P.25, R.283 Ligands: ZN.1, PG0.39 Ligand excluded by PLIP PG0.38: 9 residues within 4Å: Chain A: E.22, D.24, F.27, K.33, E.276, H.279, D.280 Ligands: PG0.39, PG0.40 Ligand excluded by PLIP PG0.39: 8 residues within 4Å: Chain A: E.21, E.22, E.23, D.24, P.25 Ligands: PG0.37, PG0.38, PG0.40 Ligand excluded by PLIP PG0.40: 11 residues within 4Å: Chain A: L.19, V.20, E.21, E.22, E.23, K.33, L.92, I.93, S.94 Ligands: PG0.38, PG0.39 Ligand excluded by PLIP PG0.41: 5 residues within 4Å: Chain A: S.132, S.133, V.135, A.136, R.145 Ligand excluded by PLIP PG0.42: 6 residues within 4Å: Chain A: P.54, T.55, Q.264, N.265, L.266, T.267 Ligand excluded by PLIP PG0.43: 1 residues within 4Å: Chain A: D.238 Ligand excluded by PLIP PG0.44: 2 residues within 4Å: Chain A: S.15, T.16 Ligand excluded by PLIP PG0.45: 4 residues within 4Å: Chain A: R.232, R.283, E.284, K.286 Ligand excluded by PLIP PG0.46: 3 residues within 4Å: Chain A: G.350, T.351, T.352 Ligand excluded by PLIP

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Pigment epithelium-derived factor

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