SMTL ID : 4i49.1

Structure of ngNAGS bound with bisubstrate analog CoA-NAG

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-hexamer

Ligands

6 x 1C4: (2S)-2-({(3S,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14,20-trioxo-2,4,6-trioxa-18-thia-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaicosan-20-yl}amino)pentanedioic acid (non-preferred name)(Non-covalent)

1C4.1: 33 residues within 4Å: Chain A: L.327, I.332, L.333, L.334, R.336, I.374, A.375, C.376, 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, R.436, R.445, S.447 Chain C: R.154, R.171, K.172, Y.197 31 PLIP interactions: 4 interactions with chain C, 27 interactions with chain A Hydrogen bonds: C:R.171, C:Y.197, A:L.334, A:C.376, A:L.377, A:L.377, A:V.379, A:Q.384, A:D.385, A:D.385, A:D.385, A:G.387, A:G.389, A:E.390, A:L.411, A:N.414, A:W.418, A:R.422, A:S.447 Salt bridges: C:R.171, C:K.172, A:R.336, A:R.422, A:R.436, A:R.445 Hydrophobic interactions: A:I.332, A:L.334, A:L.377 Water bridges: A:R.436, A:R.436 pi-Stacking: A:W.418 1C4.3: 33 residues within 4Å: Chain A: R.154, R.171, K.172, Y.197 Chain B: L.327, I.332, L.333, L.334, R.336, I.374, A.375, C.376, 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, R.436, R.445, S.447 31 PLIP interactions: 27 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.332, B:L.334, B:L.377 Hydrogen bonds: B:L.334, B:C.376, B:L.377, B:L.377, B:V.379, B:Q.384, B:D.385, B:D.385, B:D.385, B:G.387, B:G.389, B:E.390, B:L.411, B:N.414, B:W.418, B:R.422, B:S.447, A:R.171, A:Y.197 Water bridges: B:R.436, B:R.436 Salt bridges: B:R.336, B:R.422, B:R.436, B:R.445, A:R.171, A:K.172 pi-Stacking: B:W.418 1C4.5: 33 residues within 4Å: Chain B: R.154, R.171, K.172, Y.197 Chain C: L.327, I.332, L.333, L.334, R.336, I.374, A.375, C.376, 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, R.436, R.445, S.447 31 PLIP interactions: 4 interactions with chain B, 27 interactions with chain C Hydrogen bonds: B:R.171, B:Y.197, C:L.334, C:C.376, C:L.377, C:L.377, C:V.379, C:Q.384, C:D.385, C:D.385, C:D.385, C:G.387, C:G.389, C:E.390, C:L.411, C:N.414, C:W.418, C:R.422, C:S.447 Salt bridges: B:R.171, B:K.172, C:R.336, C:R.422, C:R.436, C:R.445 Hydrophobic interactions: C:I.332, C:L.334, C:L.377 Water bridges: C:R.436, C:R.436 pi-Stacking: C:W.418 1C4.7: 33 residues within 4Å: Chain D: L.327, I.332, L.333, L.334, R.336, I.374, A.375, C.376, 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, R.436, R.445, S.447 Chain F: R.154, R.171, K.172, Y.197 32 PLIP interactions: 27 interactions with chain D, 5 interactions with chain F Hydrophobic interactions: D:I.332, D:L.334, D:L.377 Hydrogen bonds: D:L.334, D:C.376, D:L.377, D:L.377, D:V.379, D:Q.384, D:D.385, D:D.385, D:G.387, D:G.389, D:E.390, D:L.411, D:N.414, D:W.418, D:R.422, D:S.447, F:R.171, F:Y.197, F:Y.197 Water bridges: D:E.373, D:R.436, D:R.436 Salt bridges: D:R.336, D:R.422, D:R.436, D:R.445, F:R.171, F:K.172 pi-Stacking: D:W.418 1C4.9: 33 residues within 4Å: Chain D: R.154, R.171, K.172, Y.197 Chain E: L.327, I.332, L.333, L.334, R.336, I.374, A.375, C.376, 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, R.436, R.445, S.447 32 PLIP interactions: 27 interactions with chain E, 5 interactions with chain D Hydrophobic interactions: E:I.332, E:L.334, E:L.377 Hydrogen bonds: E:L.334, E:C.376, E:L.377, E:L.377, E:V.379, E:Q.384, E:D.385, E:D.385, E:G.387, E:G.389, E:E.390, E:L.411, E:N.414, E:W.418, E:R.422, E:S.447, D:R.171, D:Y.197, D:Y.197 Water bridges: E:E.373, E:R.436, E:R.436 Salt bridges: E:R.336, E:R.422, E:R.436, E:R.445, D:R.171, D:K.172 pi-Stacking: E:W.418 1C4.11: 33 residues within 4Å: Chain E: R.154, R.171, K.172, Y.197 Chain F: L.327, I.332, L.333, L.334, R.336, I.374, A.375, C.376, 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, R.436, R.445, S.447 32 PLIP interactions: 27 interactions with chain F, 5 interactions with chain E Hydrophobic interactions: F:I.332, F:L.334, F:L.377 Hydrogen bonds: F:L.334, F:C.376, F:L.377, F:L.377, F:V.379, F:Q.384, F:D.385, F:D.385, F:G.387, F:G.389, F:E.390, F:L.411, F:N.414, F:W.418, F:R.422, F:S.447, E:R.171, E:Y.197, E:Y.197 Water bridges: F:E.373, F:R.436, F:R.436 Salt bridges: F:R.336, F:R.422, F:R.436, F:R.445, E:R.171, E:K.172 pi-Stacking: F:W.418

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 10 residues within 4Å: Chain A: K.62, L.63, D.66, G.281, A.283, D.284, G.285, S.286, L.287 Chain D: R.32 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:D.66, A:D.66, A:G.281, A:D.284, A:G.285, A:L.287 Salt bridges: D:R.32 SO4.4: 10 residues within 4Å: Chain B: K.62, L.63, D.66, G.281, A.283, D.284, G.285, S.286, L.287 Chain F: R.32 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:D.66, B:D.66, B:G.281, B:D.284, B:G.285, B:L.287 Salt bridges: F:R.32 SO4.6: 10 residues within 4Å: Chain C: K.62, L.63, D.66, G.281, A.283, D.284, G.285, S.286, L.287 Chain E: R.32 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:D.66, C:D.66, C:G.281, C:D.284, C:G.285, C:L.287 Salt bridges: E:R.32 SO4.8: 10 residues within 4Å: Chain A: R.32 Chain D: K.62, L.63, D.66, G.281, A.283, D.284, G.285, S.286, L.287 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:D.66, D:G.281, D:G.285, D:L.287 Salt bridges: A:R.32 SO4.10: 10 residues within 4Å: Chain C: R.32 Chain E: K.62, L.63, D.66, G.281, A.283, D.284, G.285, S.286, L.287 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain E Salt bridges: C:R.32 Hydrogen bonds: E:D.66, E:G.281, E:G.285, E:L.287 SO4.12: 10 residues within 4Å: Chain B: R.32 Chain F: K.62, L.63, D.66, G.281, A.283, D.284, G.285, S.286, L.287 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain F Salt bridges: B:R.32 Hydrogen bonds: F:D.66, F:G.281, F:G.285, F:L.287

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, G. et al., Structure of the complex of Neisseria gonorrhoeae N-acetyl-l-glutamate synthase with a bound bisubstrate analog. Biochem.Biophys.Res.Commun. (2013)

Release Date

2013-01-09

Peptides

Amino-acid acetyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Amino-acid acetyltransferase

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