SMTL ID : 7cqn.1

GmaS in complex with AMPPCP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-12-mer

Ligands

12 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.1: 15 residues within 4Å: Chain A: K.138, G.140, E.142, Y.194, Q.195, W.209, D.210, Y.211, H.257, L.258, S.259, R.332, R.337, G.342, R.343 28 PLIP interactions: 25 interactions with chain A, 3 interactions with chain F Hydrogen bonds: A:G.140, A:Y.194, A:Q.195, A:W.209, A:Y.211, A:S.259, A:S.259, A:N.267, A:R.332, A:R.332, A:R.337, A:R.337, A:R.343 Water bridges: A:V.141, A:Q.195, A:E.206, A:W.209, A:W.209, A:D.210, A:H.255, F:G.66, F:G.66, F:D.82 Salt bridges: A:H.257, A:R.343 pi-Stacking: A:Y.211, A:Y.211 pi-Cation interactions: A:R.343 ACP.2: 17 residues within 4Å: Chain A: G.66, D.82 Chain B: K.138, G.140, Y.194, Q.195, W.209, D.210, Y.211, H.257, L.258, S.259, N.267, R.332, R.337, G.342, R.343 26 PLIP interactions: 5 interactions with chain A, 21 interactions with chain B Hydrogen bonds: A:G.66, A:G.66, A:G.66, B:G.140, B:Y.194, B:Q.195, B:W.209, B:Y.211, B:S.259, B:S.259, B:N.267, B:R.332, B:R.337, B:R.337, B:R.343, B:R.343 Water bridges: A:K.50, A:K.50, B:V.141, B:W.209, B:W.209 Salt bridges: B:H.257, B:R.343 pi-Stacking: B:Y.211, B:Y.211 pi-Cation interactions: B:R.343 ACP.3: 17 residues within 4Å: Chain C: K.138, G.140, Y.194, Q.195, W.209, D.210, Y.211, H.257, L.258, S.259, N.267, R.332, R.337, G.342, R.343 Chain H: G.66, D.82 29 PLIP interactions: 23 interactions with chain C, 6 interactions with chain H Hydrogen bonds: C:G.140, C:Y.194, C:Q.195, C:W.209, C:Y.211, C:S.259, C:S.259, C:N.267, C:R.332, C:R.337, C:R.337, C:R.343, C:R.343, H:G.66, H:G.66 Water bridges: C:V.141, C:V.141, C:Q.195, C:W.209, C:D.210, H:G.66, H:G.66, H:D.82, H:D.82 Salt bridges: C:H.257, C:R.343 pi-Stacking: C:Y.211, C:Y.211 pi-Cation interactions: C:R.343 ACP.4: 15 residues within 4Å: Chain D: K.138, G.140, E.142, Y.194, Q.195, W.209, D.210, Y.211, H.257, L.258, S.259, R.332, R.337, G.342, R.343 28 PLIP interactions: 25 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:G.140, D:Y.194, D:Q.195, D:W.209, D:Y.211, D:S.259, D:S.259, D:N.267, D:R.332, D:R.332, D:R.337, D:R.337, D:R.343 Water bridges: D:V.141, D:Q.195, D:E.206, D:W.209, D:W.209, D:D.210, D:H.255, C:G.66, C:G.66, C:D.82 Salt bridges: D:H.257, D:R.343 pi-Stacking: D:Y.211, D:Y.211 pi-Cation interactions: D:R.343 ACP.5: 17 residues within 4Å: Chain D: G.66, D.82 Chain E: K.138, G.140, Y.194, Q.195, W.209, D.210, Y.211, H.257, L.258, S.259, N.267, R.332, R.337, G.342, R.343 26 PLIP interactions: 21 interactions with chain E, 5 interactions with chain D Hydrogen bonds: E:G.140, E:Y.194, E:Q.195, E:W.209, E:Y.211, E:S.259, E:S.259, E:N.267, E:R.332, E:R.337, E:R.337, E:R.343, E:R.343, D:G.66, D:G.66, D:G.66 Water bridges: E:V.141, E:W.209, E:W.209, D:K.50, D:K.50 Salt bridges: E:H.257, E:R.343 pi-Stacking: E:Y.211, E:Y.211 pi-Cation interactions: E:R.343 ACP.6: 17 residues within 4Å: Chain F: K.138, G.140, Y.194, Q.195, W.209, D.210, Y.211, H.257, L.258, S.259, N.267, R.332, R.337, G.342, R.343 Chain K: G.66, D.82 29 PLIP interactions: 6 interactions with chain K, 23 interactions with chain F Hydrogen bonds: K:G.66, K:G.66, F:G.140, F:Y.194, F:Q.195, F:W.209, F:Y.211, F:S.259, F:S.259, F:N.267, F:R.332, F:R.337, F:R.337, F:R.343, F:R.343 Water bridges: K:G.66, K:G.66, K:D.82, K:D.82, F:V.141, F:V.141, F:Q.195, F:W.209, F:D.210 Salt bridges: F:H.257, F:R.343 pi-Stacking: F:Y.211, F:Y.211 pi-Cation interactions: F:R.343 ACP.7: 15 residues within 4Å: Chain G: K.138, G.140, E.142, Y.194, Q.195, W.209, D.210, Y.211, H.257, L.258, S.259, R.332, R.337, G.342, R.343 27 PLIP interactions: 24 interactions with chain G, 3 interactions with chain L Hydrogen bonds: G:G.140, G:Y.194, G:Q.195, G:W.209, G:Y.211, G:S.259, G:S.259, G:N.267, G:R.332, G:R.332, G:R.337, G:R.337, G:R.343 Water bridges: G:V.141, G:Q.195, G:W.209, G:W.209, G:D.210, G:D.210, L:G.66, L:G.66, L:D.82 Salt bridges: G:H.257, G:R.343 pi-Stacking: G:Y.211, G:Y.211 pi-Cation interactions: G:R.343 ACP.8: 17 residues within 4Å: Chain G: G.66, D.82 Chain H: K.138, G.140, Y.194, Q.195, W.209, D.210, Y.211, H.257, L.258, S.259, N.267, R.332, R.337, G.342, R.343 27 PLIP interactions: 22 interactions with chain H, 5 interactions with chain G Hydrogen bonds: H:G.140, H:Y.194, H:Q.195, H:W.209, H:Y.211, H:S.259, H:S.259, H:N.267, H:R.332, H:R.337, H:R.337, H:R.343, H:R.343, G:G.66, G:G.66, G:G.66 Water bridges: H:V.141, H:W.209, H:W.209, H:D.210, G:K.50, G:K.50 Salt bridges: H:H.257, H:R.343 pi-Stacking: H:Y.211, H:Y.211 pi-Cation interactions: H:R.343 ACP.9: 17 residues within 4Å: Chain B: G.66, D.82 Chain I: K.138, G.140, Y.194, Q.195, W.209, D.210, Y.211, H.257, L.258, S.259, N.267, R.332, R.337, G.342, R.343 29 PLIP interactions: 21 interactions with chain I, 8 interactions with chain B Hydrogen bonds: I:G.140, I:Y.194, I:Q.195, I:W.209, I:Y.211, I:S.259, I:S.259, I:N.267, I:R.332, I:R.337, I:R.337, I:R.343, I:R.343, B:G.66, B:G.66 Water bridges: I:V.141, I:V.141, I:W.209, B:K.50, B:G.66, B:G.66, B:D.82, B:D.82, B:D.82 Salt bridges: I:H.257, I:R.343 pi-Stacking: I:Y.211, I:Y.211 pi-Cation interactions: I:R.343 ACP.10: 15 residues within 4Å: Chain J: K.138, G.140, E.142, Y.194, Q.195, W.209, D.210, Y.211, H.257, L.258, S.259, R.332, R.337, G.342, R.343 27 PLIP interactions: 24 interactions with chain J, 3 interactions with chain I Hydrogen bonds: J:G.140, J:Y.194, J:Q.195, J:W.209, J:Y.211, J:S.259, J:S.259, J:N.267, J:R.332, J:R.332, J:R.337, J:R.337, J:R.343 Water bridges: J:V.141, J:Q.195, J:W.209, J:W.209, J:D.210, J:D.210, I:G.66, I:G.66, I:D.82 Salt bridges: J:H.257, J:R.343 pi-Stacking: J:Y.211, J:Y.211 pi-Cation interactions: J:R.343 ACP.11: 17 residues within 4Å: Chain J: G.66, D.82 Chain K: K.138, G.140, Y.194, Q.195, W.209, D.210, Y.211, H.257, L.258, S.259, N.267, R.332, R.337, G.342, R.343 27 PLIP interactions: 22 interactions with chain K, 5 interactions with chain J Hydrogen bonds: K:G.140, K:Y.194, K:Q.195, K:W.209, K:Y.211, K:S.259, K:S.259, K:N.267, K:R.332, K:R.337, K:R.337, K:R.343, K:R.343, J:G.66, J:G.66, J:G.66 Water bridges: K:V.141, K:W.209, K:W.209, K:D.210, J:K.50, J:K.50 Salt bridges: K:H.257, K:R.343 pi-Stacking: K:Y.211, K:Y.211 pi-Cation interactions: K:R.343 ACP.12: 17 residues within 4Å: Chain E: G.66, D.82 Chain L: K.138, G.140, Y.194, Q.195, W.209, D.210, Y.211, H.257, L.258, S.259, N.267, R.332, R.337, G.342, R.343 29 PLIP interactions: 21 interactions with chain L, 8 interactions with chain E Hydrogen bonds: L:G.140, L:Y.194, L:Q.195, L:W.209, L:Y.211, L:S.259, L:S.259, L:N.267, L:R.332, L:R.337, L:R.337, L:R.343, L:R.343, E:G.66, E:G.66 Water bridges: L:V.141, L:V.141, L:W.209, E:K.50, E:G.66, E:G.66, E:D.82, E:D.82, E:D.82 Salt bridges: L:H.257, L:R.343 pi-Stacking: L:Y.211, L:Y.211 pi-Cation interactions: L:R.343

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, N. et al., Crystal structures of gamma-glutamylmethylamide synthetase provide insight into bacterial metabolism of oceanic monomethylamine. J.Biol.Chem. (2020)

Release Date

2020-11-18

Peptides

Type III glutamate--ammonia ligase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

G
A

H
B

I
C

J
A

K
B

L
C

Type III glutamate--ammonia ligase

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