SMTL ID : 8zok.1

EcGPR tetramer with catalytic intermediates

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 22 residues within 4Å: Chain A: M.62, R.65, Y.119, E.120, R.143, G.145, K.146, R.181, V.184, R.200, G.201, G.202, L.205, L.208, G.220, G.221, G.223, C.253, E.312, V.386 Ligands: PO4.2, VHF.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.119, A:K.146, A:G.202, A:G.221, A:G.223, A:E.312, A:V.386 Salt bridges: A:R.65, A:R.143, A:R.181 pi-Cation interactions: A:R.181 NAP.4: 20 residues within 4Å: Chain B: R.65, Y.119, E.120, R.143, K.146, R.181, V.184, R.200, G.201, G.202, L.205, L.208, G.220, G.221, G.223, C.253, E.312, V.386 Ligands: PO4.5, VHF.6 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Y.119, B:K.146, B:G.202, B:G.221, B:G.223, B:E.312, B:V.386 Salt bridges: B:R.65, B:R.143, B:R.181 pi-Cation interactions: B:R.181 NAP.7: 21 residues within 4Å: Chain C: R.65, Y.119, E.120, R.143, G.145, K.146, R.181, V.184, R.200, G.201, G.202, L.205, L.208, G.220, G.221, G.223, C.253, E.312, V.386 Ligands: PO4.8, VHF.9 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:Y.119, C:K.146, C:R.181, C:G.202, C:G.223, C:E.312, C:V.386, C:V.386 Salt bridges: C:R.65, C:R.143, C:R.181 pi-Cation interactions: C:R.181 NAP.10: 22 residues within 4Å: Chain D: M.62, R.65, Y.119, E.120, R.143, G.145, K.146, R.181, R.200, G.201, G.202, L.205, L.208, G.220, G.221, I.222, G.223, C.253, E.312, V.386 Ligands: PO4.11, VHF.12 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:Y.119, D:A.121, D:K.146, D:G.202, D:G.221, D:G.223, D:E.312, D:V.386 Salt bridges: D:R.65, D:R.143, D:R.181 pi-Cation interactions: D:R.181

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 8 residues within 4Å: Chain A: R.65, E.120, R.122, R.200, T.252, C.253 Ligands: NAP.1, VHF.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.200, A:R.249 Water bridges: A:R.65, A:S.251 Salt bridges: A:R.65, A:R.122 PO4.5: 8 residues within 4Å: Chain B: R.65, E.120, R.122, R.200, T.252, C.253 Ligands: NAP.4, VHF.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.200 Water bridges: B:R.65, B:S.251 Salt bridges: B:R.122 PO4.8: 8 residues within 4Å: Chain C: R.65, E.120, R.122, R.200, T.252, C.253 Ligands: NAP.7, VHF.9 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.65, C:E.120, C:R.200 Water bridges: C:S.251, C:T.252 Salt bridges: C:R.122 PO4.11: 8 residues within 4Å: Chain D: R.65, E.120, R.122, R.200, T.252, C.253 Ligands: NAP.10, VHF.12 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.65, D:E.120, D:R.200, D:R.249 Water bridges: D:S.251, D:T.252 Salt bridges: D:R.122

4 x VHF: (2~{S})-2-azanyl-5-oxidanylidene-5-phosphonooxy-pentanoic acid(Covalent)

VHF.3: 11 residues within 4Å: Chain A: T.252, C.253, N.254, H.340, R.371, T.373, D.374, E.383, V.386 Ligands: NAP.1, PO4.2 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.254, A:N.254, A:D.374 Salt bridges: A:R.371, B:R.416 VHF.6: 10 residues within 4Å: Chain B: T.252, C.253, N.254, H.340, T.373, D.374, E.383, V.386 Ligands: NAP.4, PO4.5 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.254, B:N.254, B:T.373, B:D.374 Salt bridges: B:R.371, A:R.416 VHF.9: 10 residues within 4Å: Chain C: T.252, C.253, N.254, H.340, R.371, T.373, D.374, E.383 Ligands: NAP.7, PO4.8 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.254, C:D.374 Salt bridges: C:R.371, D:R.416 VHF.12: 11 residues within 4Å: Chain D: T.252, C.253, N.254, H.340, R.371, T.373, D.374, E.383, V.386 Ligands: NAP.10, PO4.11 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain D Salt bridges: C:R.416, D:R.371 Hydrogen bonds: D:N.254, D:T.373, D:D.374, D:E.383

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, T. et al., EcGPR tetramer with catalytic intermediates. To Be Published

Release Date

2025-06-04

Peptides

Gamma-glutamyl phosphate reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Gamma-glutamyl phosphate reductase

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