SMTL ID : 3d2p.1

Crystal structure of N-acetylglutamate synthase from Neisseria gonorrhoeae complexed with coenzyme A and L-arginine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

homo-hexamer

Ligands

6 x COA: COENZYME A(Non-covalent)

COA.1: 16 residues within 4Å: Chain A: L.327, L.377, A.378, V.379, Q.384, D.385, G.386, G.387, Y.388, G.389, E.390, N.414, T.415, E.417, W.418, R.422 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.327, A:V.379, A:T.415 Hydrogen bonds: A:D.385, A:G.386, A:G.387, A:Y.388, A:G.389, A:E.390, A:N.414, A:E.417, A:W.418 Salt bridges: A:R.422 pi-Stacking: A:W.418 COA.3: 15 residues within 4Å: Chain B: L.327, L.377, V.379, Q.384, D.385, G.386, G.387, Y.388, G.389, E.390, N.414, T.415, E.417, W.418, R.422 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.327, B:V.379, B:T.415, B:W.418 Hydrogen bonds: B:D.385, B:D.385, B:G.386, B:G.387, B:Y.388, B:G.389, B:E.390, B:N.414, B:W.418, B:R.422 pi-Stacking: B:W.418 COA.5: 16 residues within 4Å: Chain C: L.327, L.377, A.378, V.379, Q.384, D.385, G.386, G.387, Y.388, G.389, E.390, N.414, T.415, E.417, W.418, R.422 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:L.327, C:V.379, C:T.415 Hydrogen bonds: C:D.385, C:G.386, C:G.387, C:Y.388, C:G.389, C:E.390, C:N.414, C:E.417, C:W.418 Salt bridges: C:R.422 pi-Stacking: C:W.418 COA.7: 15 residues within 4Å: Chain D: L.327, L.377, V.379, Q.384, D.385, G.386, G.387, Y.388, G.389, E.390, N.414, T.415, E.417, W.418, R.422 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:L.327, D:V.379, D:T.415, D:W.418 Hydrogen bonds: D:D.385, D:D.385, D:G.386, D:G.387, D:Y.388, D:G.389, D:E.390, D:N.414, D:W.418, D:R.422 pi-Stacking: D:W.418 COA.9: 16 residues within 4Å: Chain E: L.327, L.377, A.378, V.379, Q.384, D.385, G.386, G.387, Y.388, G.389, E.390, N.414, T.415, E.417, W.418, R.422 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:L.327, E:V.379, E:T.415 Hydrogen bonds: E:D.385, E:G.386, E:G.387, E:Y.388, E:G.389, E:E.390, E:N.414, E:E.417, E:W.418 Salt bridges: E:R.422 pi-Stacking: E:W.418 COA.11: 15 residues within 4Å: Chain F: L.327, L.377, V.379, Q.384, D.385, G.386, G.387, Y.388, G.389, E.390, N.414, T.415, E.417, W.418, R.422 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:L.327, F:V.379, F:T.415, F:W.418 Hydrogen bonds: F:D.385, F:D.385, F:G.386, F:G.387, F:Y.388, F:G.389, F:E.390, F:N.414, F:W.418, F:R.422 pi-Stacking: F:W.418

6 x ARG: ARGININE(Non-covalent)

ARG.2: 17 residues within 4Å: Chain A: Y.37, K.221, E.240, T.241, Q.277, E.290, L.291, F.292, T.293, R.294, N.295, G.296, I.297, G.298, T.299, S.300, D.354 9 PLIP interactions: 9 interactions with chain A, Hydrogen bonds: A:E.240, A:Q.277, A:L.291, A:T.293, A:G.298 Water bridges: A:D.354, A:D.354 Salt bridges: A:K.221, A:E.290 ARG.4: 16 residues within 4Å: Chain B: Y.37, K.221, E.240, T.241, Q.277, E.290, L.291, T.293, R.294, N.295, G.296, I.297, G.298, T.299, S.300, D.354 8 PLIP interactions: 8 interactions with chain B, Hydrogen bonds: B:E.240, B:E.240, B:Q.277, B:L.291 Water bridges: B:R.275, B:D.354 Salt bridges: B:K.221, B:E.290 ARG.6: 17 residues within 4Å: Chain C: Y.37, K.221, E.240, T.241, Q.277, E.290, L.291, F.292, T.293, R.294, N.295, G.296, I.297, G.298, T.299, S.300, D.354 9 PLIP interactions: 9 interactions with chain C, Hydrogen bonds: C:E.240, C:Q.277, C:L.291, C:T.293, C:G.298 Water bridges: C:D.354, C:D.354 Salt bridges: C:K.221, C:E.290 ARG.8: 16 residues within 4Å: Chain D: Y.37, K.221, E.240, T.241, Q.277, E.290, L.291, T.293, R.294, N.295, G.296, I.297, G.298, T.299, S.300, D.354 8 PLIP interactions: 8 interactions with chain D, Hydrogen bonds: D:E.240, D:E.240, D:Q.277, D:L.291 Water bridges: D:R.275, D:D.354 Salt bridges: D:K.221, D:E.290 ARG.10: 17 residues within 4Å: Chain E: Y.37, K.221, E.240, T.241, Q.277, E.290, L.291, F.292, T.293, R.294, N.295, G.296, I.297, G.298, T.299, S.300, D.354 9 PLIP interactions: 9 interactions with chain E, Hydrogen bonds: E:E.240, E:Q.277, E:L.291, E:T.293, E:G.298 Water bridges: E:D.354, E:D.354 Salt bridges: E:K.221, E:E.290 ARG.12: 16 residues within 4Å: Chain F: Y.37, K.221, E.240, T.241, Q.277, E.290, L.291, T.293, R.294, N.295, G.296, I.297, G.298, T.299, S.300, D.354 8 PLIP interactions: 8 interactions with chain F, Hydrogen bonds: F:E.240, F:E.240, F:Q.277, F:L.291 Water bridges: F:R.275, F:D.354 Salt bridges: F:K.221, F:E.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Min, L. et al., Mechanism of Allosteric Inhibition of N-Acetyl-L-glutamate Synthase by L-Arginine. J.Biol.Chem. (2009)

Release Date

2008-12-23

Peptides

Putative acetylglutamate synthase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Putative acetylglutamate synthase

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