SMTL ID : 3d2m.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

homo-hexamer

Ligands

6 x COA: COENZYME A(Non-covalent)

COA.1: 25 residues within 4Å: Chain A: L.327, I.332, L.377, A.378, V.379, Q.384, D.385, G.386, G.387, Y.388, G.389, E.390, L.411, S.412, N.414, T.415, E.417, W.418, F.419, R.422 Chain B: R.154, R.171, K.172, Y.197 Ligands: GLU.2 21 PLIP interactions: 3 interactions with chain B, 18 interactions with chain A Hydrogen bonds: B:Y.197, A:V.379, A:D.385, A:D.385, A:D.385, A:G.387, A:G.389, A:E.390, A:N.414, A:T.415, A:W.418, A:R.422, A:R.422 Salt bridges: B:R.171, B:K.172 Hydrophobic interactions: A:L.377, A:T.415, A:W.418 Water bridges: A:Q.384, A:Q.384 pi-Stacking: A:W.418 COA.3: 25 residues within 4Å: Chain B: L.327, I.332, L.377, A.378, V.379, Q.384, D.385, G.386, G.387, Y.388, G.389, E.390, L.411, S.412, N.414, T.415, E.417, W.418, F.419, R.422 Chain C: R.154, R.171, K.172, Y.197 Ligands: GLU.4 21 PLIP interactions: 18 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:L.377, B:T.415, B:W.418 Hydrogen bonds: B:V.379, B:D.385, B:D.385, B:D.385, B:G.387, B:G.389, B:E.390, B:N.414, B:T.415, B:W.418, B:R.422, B:R.422, C:Y.197 Water bridges: B:Q.384, B:Q.384 pi-Stacking: B:W.418 Salt bridges: C:R.171, C:K.172 COA.5: 25 residues within 4Å: Chain A: R.154, R.171, K.172, Y.197 Chain C: L.327, I.332, L.377, A.378, V.379, Q.384, D.385, G.386, G.387, Y.388, G.389, E.390, L.411, S.412, N.414, T.415, E.417, W.418, F.419, R.422 Ligands: GLU.6 21 PLIP interactions: 18 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:L.377, C:T.415, C:W.418 Hydrogen bonds: C:V.379, C:D.385, C:D.385, C:D.385, C:G.387, C:G.389, C:E.390, C:N.414, C:T.415, C:W.418, C:R.422, C:R.422, A:Y.197 Water bridges: C:Q.384, C:Q.384 pi-Stacking: C:W.418 Salt bridges: A:R.171, A:K.172 COA.7: 25 residues within 4Å: Chain D: L.327, I.332, L.377, A.378, V.379, Q.384, D.385, G.386, G.387, Y.388, G.389, E.390, L.411, S.412, N.414, T.415, E.417, W.418, F.419, R.422 Chain E: R.154, R.171, K.172, Y.197 Ligands: GLU.8 19 PLIP interactions: 17 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:L.377, D:T.415, D:W.418 Hydrogen bonds: D:V.379, D:D.385, D:D.385, D:G.387, D:G.389, D:E.390, D:E.390, D:N.414, D:W.418, D:R.422, D:R.422 Water bridges: D:Q.384, D:Q.384 pi-Stacking: D:W.418 Salt bridges: E:R.171, E:K.172 COA.9: 25 residues within 4Å: Chain E: L.327, I.332, L.377, A.378, V.379, Q.384, D.385, G.386, G.387, Y.388, G.389, E.390, L.411, S.412, N.414, T.415, E.417, W.418, F.419, R.422 Chain F: R.154, R.171, K.172, Y.197 Ligands: GLU.10 19 PLIP interactions: 2 interactions with chain F, 17 interactions with chain E Salt bridges: F:R.171, F:K.172 Hydrophobic interactions: E:L.377, E:T.415, E:W.418 Hydrogen bonds: E:V.379, E:D.385, E:D.385, E:G.387, E:G.389, E:E.390, E:E.390, E:N.414, E:W.418, E:R.422, E:R.422 Water bridges: E:Q.384, E:Q.384 pi-Stacking: E:W.418 COA.11: 25 residues within 4Å: Chain D: R.154, R.171, K.172, Y.197 Chain F: L.327, I.332, L.377, A.378, V.379, Q.384, D.385, G.386, G.387, Y.388, G.389, E.390, L.411, S.412, N.414, T.415, E.417, W.418, F.419, R.422 Ligands: GLU.12 19 PLIP interactions: 17 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: F:L.377, F:T.415, F:W.418 Hydrogen bonds: F:V.379, F:D.385, F:D.385, F:G.387, F:G.389, F:E.390, F:E.390, F:N.414, F:W.418, F:R.422, F:R.422 Water bridges: F:Q.384, F:Q.384 pi-Stacking: F:W.418 Salt bridges: D:R.171, D:K.172

6 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.2: 11 residues within 4Å: Chain A: I.332, L.333, L.334, R.336, A.375, C.376, L.411, R.436, R.445, S.447 Ligands: COA.1 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:L.334 Hydrogen bonds: A:L.334, A:C.376, A:L.411, A:S.447 Water bridges: A:L.411 Salt bridges: A:R.336, A:R.436, A:R.445 GLU.4: 11 residues within 4Å: Chain B: I.332, L.333, L.334, R.336, A.375, C.376, L.411, R.436, R.445, S.447 Ligands: COA.3 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:L.334 Hydrogen bonds: B:L.334, B:C.376, B:L.411, B:S.447 Water bridges: B:L.411 Salt bridges: B:R.336, B:R.436, B:R.445 GLU.6: 11 residues within 4Å: Chain C: I.332, L.333, L.334, R.336, A.375, C.376, L.411, R.436, R.445, S.447 Ligands: COA.5 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:L.334 Hydrogen bonds: C:L.334, C:C.376, C:L.411, C:S.447 Water bridges: C:L.411 Salt bridges: C:R.336, C:R.436, C:R.445 GLU.8: 11 residues within 4Å: Chain D: I.332, L.333, L.334, R.336, A.375, C.376, L.411, R.436, R.445, S.447 Ligands: COA.7 9 PLIP interactions: 9 interactions with chain D, Hydrophobic interactions: D:L.334 Hydrogen bonds: D:L.334, D:C.376, D:L.411, D:S.447 Water bridges: D:L.411 Salt bridges: D:R.336, D:R.436, D:R.445 GLU.10: 11 residues within 4Å: Chain E: I.332, L.333, L.334, R.336, A.375, C.376, L.411, R.436, R.445, S.447 Ligands: COA.9 9 PLIP interactions: 9 interactions with chain E, Hydrophobic interactions: E:L.334 Hydrogen bonds: E:L.334, E:C.376, E:L.411, E:S.447 Water bridges: E:L.411 Salt bridges: E:R.336, E:R.436, E:R.445 GLU.12: 11 residues within 4Å: Chain F: I.332, L.333, L.334, R.336, A.375, C.376, L.411, R.436, R.445, S.447 Ligands: COA.11 9 PLIP interactions: 9 interactions with chain F, Hydrophobic interactions: F:L.334 Hydrogen bonds: F:L.334, F:C.376, F:L.411, F:S.447 Water bridges: F:L.411 Salt bridges: F:R.336, F:R.436, F:R.445

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
A

C
A

D
A

E
A

F
A

Putative acetylglutamate synthase

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