SMTL ID : 1gpm.1

ESCHERICHIA COLI GMP SYNTHETASE COMPLEXED WITH AMP AND PYROPHOSPHATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 4 residues within 4Å: Chain A: K.517, T.521, I.522, E.523 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.522, A:E.523 Salt bridges: A:K.517 PO4.2: 4 residues within 4Å: Chain B: K.517, T.521, I.522, E.523 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.522, B:E.523, B:E.523 Salt bridges: B:K.517 PO4.4: 4 residues within 4Å: Chain C: K.517, T.521, I.522, E.523 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.521, C:I.522, C:E.523 Salt bridges: C:K.517 PO4.6: 4 residues within 4Å: Chain D: K.517, T.521, I.522, E.523 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:I.522, D:E.523 Salt bridges: D:K.517

3 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.3: 2 residues within 4Å: Ligands: POP.11, AMP.12 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: AMP.12, H2O.321 MG.5: 3 residues within 4Å: Chain C: D.239 Ligands: POP.14, AMP.15 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: AMP.15, H2O.598 MG.7: 3 residues within 4Å: Chain D: D.239 Ligands: POP.17, AMP.18 No protein-ligand interaction detected (PLIP)

4 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.8: 7 residues within 4Å: Chain A: S.235, G.237, V.238, D.239, S.240, K.381 Ligands: AMP.9 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.235, A:V.238, A:D.239, A:S.240 Water bridges: A:D.239, A:G.335, A:R.400, A:F.403 Salt bridges: A:K.381 POP.11: 8 residues within 4Å: Chain B: S.235, G.237, V.238, D.239, S.240, K.381 Ligands: MG.3, AMP.12 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.235, B:S.235, B:G.237, B:V.238, B:D.239, B:D.239, B:S.240 Water bridges: B:F.403 Salt bridges: B:K.381 POP.14: 8 residues within 4Å: Chain C: S.235, G.237, V.238, D.239, S.240, K.381 Ligands: MG.5, AMP.15 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.235, C:S.235, C:G.237, C:V.238, C:D.239, C:D.239, C:S.240 Water bridges: C:D.239, C:D.239 Salt bridges: C:K.381 POP.17: 8 residues within 4Å: Chain D: S.235, G.237, V.238, D.239, S.240, K.381 Ligands: MG.7, AMP.18 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:S.235, D:S.235, D:G.237, D:V.238, D:D.239, D:D.239, D:S.240 Water bridges: D:K.381, D:F.403 Salt bridges: D:K.381

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.9: 9 residues within 4Å: Chain A: G.233, L.234, S.235, S.240, V.258, V.260, F.315, G.405 Ligands: POP.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.260, A:V.260 Water bridges: A:G.233, A:G.335 AMP.12: 10 residues within 4Å: Chain B: G.233, L.234, S.235, S.240, V.258, F.259, V.260, F.315 Ligands: MG.3, POP.11 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.233, B:V.260, B:V.260 Water bridges: B:S.235, B:S.235, B:F.403 AMP.15: 10 residues within 4Å: Chain C: G.233, L.234, S.235, S.240, V.258, F.259, V.260, F.315 Ligands: MG.5, POP.14 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.235, C:V.260, C:V.260 Water bridges: C:G.233 AMP.18: 11 residues within 4Å: Chain D: G.233, L.234, S.235, S.240, V.258, F.259, V.260, F.315, G.405 Ligands: MG.7, POP.17 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.235, D:V.260, D:V.260 Water bridges: D:G.233, D:G.405, D:G.405

4 x CIT: CITRIC ACID(Non-functional Binders)

CIT.10: 10 residues within 4Å: Chain A: S.17, Q.18, G.58, G.59, P.60, C.86, Y.87, F.108, S.142, H.181 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Q.18, A:Q.18, A:G.59, A:G.59, A:Y.87, A:S.142, A:S.142 Water bridges: A:G.59, A:G.144, A:G.144 Salt bridges: A:H.181 CIT.13: 10 residues within 4Å: Chain B: S.17, Q.18, G.58, G.59, P.60, C.86, Y.87, F.108, S.142, H.181 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.18, B:Q.18, B:G.59, B:G.59, B:Y.87, B:S.142, B:S.142 Water bridges: B:G.58 Salt bridges: B:H.181 CIT.16: 10 residues within 4Å: Chain C: S.17, Q.18, G.58, G.59, P.60, C.86, Y.87, F.108, S.142, H.181 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Q.18, C:Q.18, C:G.59, C:G.59, C:Y.87, C:S.142, C:S.142 Salt bridges: C:H.181 CIT.19: 11 residues within 4Å: Chain D: S.17, Q.18, G.58, G.59, P.60, C.86, Y.87, R.106, F.108, S.142, H.181 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:Q.18, D:Q.18, D:G.59, D:G.59, D:Y.87, D:S.142, D:S.142 Water bridges: D:G.58, D:G.144 Salt bridges: D:R.106, D:H.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tesmer, J.J. et al., The crystal structure of GMP synthetase reveals a novel catalytic triad and is a structural paradigm for two enzyme families. Nat.Struct.Biol. (1996)

Release Date

1996-01-29

Peptides

GMP SYNTHETASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

GMP SYNTHETASE