SMTL ID : 3seq.1

Crystal structure of C176A mutant of glutamine-dependent NAD+ synthetase from M. tuberculosis in complex with AMPCPP and NaAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.73 Å

Oligo State

homo-octamer

Ligands

8 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.1: 13 residues within 4Å: Chain A: G.367, V.368, S.369, G.371, L.372, D.373, S.374, F.398, A.399, L.400, R.463, T.481 Ligands: DND.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.369, A:L.372, A:D.373, A:D.373, A:S.374, A:L.400 Water bridges: A:E.542 APC.3: 13 residues within 4Å: Chain B: G.367, V.368, S.369, G.371, L.372, D.373, S.374, F.398, A.399, L.400, R.463, T.481 Ligands: DND.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.369, B:G.371, B:D.373, B:S.374, B:L.400, B:T.481 Water bridges: B:L.372, B:R.463, B:E.542 APC.6: 13 residues within 4Å: Chain C: G.367, V.368, S.369, G.371, L.372, D.373, S.374, F.398, A.399, L.400, R.463, T.481 Ligands: DND.7 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.369, C:G.371, C:L.372, C:D.373, C:S.374, C:L.400, C:R.463, C:T.481 APC.8: 14 residues within 4Å: Chain D: G.367, V.368, S.369, G.371, L.372, D.373, S.374, F.398, A.399, L.400, R.463, T.481, D.498 Ligands: DND.9 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.369, D:G.371, D:L.372, D:D.373, D:S.374, D:L.400, D:R.463, D:T.481, D:T.481 APC.11: 13 residues within 4Å: Chain E: G.367, V.368, S.369, G.371, L.372, D.373, S.374, F.398, A.399, L.400, R.463, T.481 Ligands: DND.12 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:S.369, E:L.372, E:D.373, E:D.373, E:D.373, E:S.374, E:L.400, E:T.481 Water bridges: E:E.542, E:E.542 APC.13: 13 residues within 4Å: Chain F: G.367, V.368, S.369, G.371, L.372, D.373, S.374, F.398, A.399, L.400, R.463, T.481 Ligands: DND.14 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:S.369, F:G.371, F:D.373, F:S.374, F:L.400, F:T.481, F:T.481 Water bridges: F:L.372, F:R.463, F:E.542 APC.16: 13 residues within 4Å: Chain G: G.367, V.368, S.369, G.371, L.372, D.373, S.374, F.398, A.399, L.400, R.463, T.481 Ligands: DND.17 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:S.369, G:G.371, G:L.372, G:D.373, G:S.374, G:L.400, G:R.463 APC.18: 14 residues within 4Å: Chain H: G.367, V.368, S.369, G.371, L.372, D.373, S.374, F.398, A.399, L.400, R.463, T.481, D.498 Ligands: DND.19 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:S.369, H:G.371, H:L.372, H:D.373, H:S.374, H:L.400, H:R.463, H:T.481

8 x DND: NICOTINIC ACID ADENINE DINUCLEOTIDE(Non-covalent)

DND.2: 20 residues within 4Å: Chain A: V.453, N.457, E.486, W.491, S.492, T.493, Y.494, D.498, F.632, F.635, K.636, S.662 Chain D: R.355, L.359, A.471, N.472, G.476, I.477, H.502 Ligands: APC.1 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:N.457, A:S.492, A:Y.494, A:S.662, D:R.355, D:N.472 Water bridges: A:F.635, D:R.469, D:R.469 Salt bridges: A:K.636, A:K.636 pi-Stacking: A:W.491, A:F.635, A:F.635 DND.4: 20 residues within 4Å: Chain B: V.453, N.457, E.486, W.491, S.492, T.493, Y.494, D.498, F.632, F.635, K.636, S.662 Chain C: R.355, L.359, A.471, N.472, G.476, I.477, H.502 Ligands: APC.3 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.457, B:W.491, B:S.492, B:S.492, B:Y.494, B:S.662, C:R.355, C:N.472 Salt bridges: B:K.636, B:K.636 pi-Stacking: B:W.491, B:F.635, B:F.635 DND.7: 18 residues within 4Å: Chain B: R.355, L.359, N.472, G.476, I.477, H.502 Chain C: N.457, E.486, W.491, S.492, T.493, Y.494, D.498, F.632, F.635, K.636, S.662 Ligands: APC.6 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:N.457, C:N.457, C:W.491, C:S.492, C:S.492, C:Y.494, C:S.662, B:R.355, B:N.472 Salt bridges: C:K.636, C:K.636 pi-Stacking: C:W.491, C:F.635, C:F.635 DND.9: 19 residues within 4Å: Chain A: R.355, L.359, A.471, N.472, G.476, I.477, H.502 Chain D: N.457, E.486, W.491, S.492, T.493, Y.494, D.498, F.632, F.635, K.636, S.662 Ligands: APC.8 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:N.457, D:S.492, D:Y.494, D:D.498, D:S.662, A:R.355, A:N.472 Water bridges: D:F.635 Salt bridges: D:K.636, D:K.636 pi-Stacking: D:W.491, D:F.635, D:F.635 DND.12: 20 residues within 4Å: Chain E: V.453, N.457, E.486, W.491, S.492, T.493, Y.494, D.498, F.632, F.635, K.636, S.662 Chain H: R.355, L.359, A.471, N.472, G.476, I.477, H.502 Ligands: APC.11 14 PLIP interactions: 4 interactions with chain H, 10 interactions with chain E Hydrogen bonds: H:R.355, H:N.472, E:N.457, E:S.492, E:Y.494, E:S.662 Water bridges: H:R.469, H:R.469, E:F.635 Salt bridges: E:K.636, E:K.636 pi-Stacking: E:W.491, E:F.635, E:F.635 DND.14: 20 residues within 4Å: Chain F: V.453, N.457, E.486, W.491, S.492, T.493, Y.494, D.498, F.632, F.635, K.636, S.662 Chain G: R.355, L.359, A.471, N.472, G.476, I.477, H.502 Ligands: APC.13 13 PLIP interactions: 11 interactions with chain F, 2 interactions with chain G Hydrogen bonds: F:N.457, F:W.491, F:S.492, F:S.492, F:Y.494, F:S.662, G:R.355, G:N.472 Salt bridges: F:K.636, F:K.636 pi-Stacking: F:W.491, F:F.635, F:F.635 DND.17: 18 residues within 4Å: Chain F: R.355, L.359, N.472, G.476, I.477, H.502 Chain G: N.457, E.486, W.491, S.492, T.493, Y.494, D.498, F.632, F.635, K.636, S.662 Ligands: APC.16 14 PLIP interactions: 12 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:N.457, G:N.457, G:W.491, G:S.492, G:S.492, G:Y.494, G:S.662, F:R.355, F:N.472 Salt bridges: G:K.636, G:K.636 pi-Stacking: G:W.491, G:F.635, G:F.635 DND.19: 19 residues within 4Å: Chain E: R.355, L.359, A.471, N.472, G.476, I.477, H.502 Chain H: N.457, E.486, W.491, S.492, T.493, Y.494, D.498, F.632, F.635, K.636, S.662 Ligands: APC.18 13 PLIP interactions: 11 interactions with chain H, 2 interactions with chain E Hydrogen bonds: H:N.457, H:S.492, H:Y.494, H:D.498, H:S.662, E:R.355, E:N.472 Water bridges: H:F.635 Salt bridges: H:K.636, H:K.636 pi-Stacking: H:W.491, H:F.635, H:F.635

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain B: Y.59, S.60, I.61, E.62, L.65, F.131, Y.132, E.133, Q.136 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.59, B:E.62, B:E.130, B:Y.132, B:Y.132, B:Q.136 GOL.10: 4 residues within 4Å: Chain D: R.219, G.255, A.256, L.257 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:L.257, B:E.212 Water bridges: D:L.257 GOL.15: 9 residues within 4Å: Chain F: Y.59, S.60, I.61, E.62, L.65, F.131, Y.132, E.133, Q.136 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:Y.59, F:E.62, F:E.130, F:Y.132, F:Y.132, F:Q.136 GOL.20: 4 residues within 4Å: Chain H: R.219, G.255, A.256, L.257 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain F Hydrogen bonds: H:L.257, F:E.212 Water bridges: H:L.257

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chuenchor, W. et al., Regulation of the intersubunit ammonia tunnel in Mycobacterium tuberculosis glutamine-dependent NAD+ synthetase. Biochem.J. (2012)

Release Date

2012-04-11

Peptides

Glutamine-dependent NAD(+) synthetase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

Glutamine-dependent NAD(+) synthetase

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