SMTL ID : 3szg.1

Crystal structure of C176A glutamine-dependent NAD+ synthetase from M. tuberculosis bound to AMP/PPi and NaAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-octamer

Ligands

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

DND.1: 20 residues within 4Å: Chain A: V.453, E.456, N.457, 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: AMP.2 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:E.456, A:N.457, A:S.492, A:Y.494, A:S.662, D:R.355, D:N.472 Salt bridges: A:K.636, A:K.636 pi-Stacking: A:F.635, A:F.635 DND.4: 21 residues within 4Å: Chain B: V.453, E.456, 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: AMP.5 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:E.456, B:N.457, 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 Water bridges: C:F.468, C:R.469 DND.8: 22 residues within 4Å: Chain B: R.355, L.359, A.471, N.472, G.476, I.477, H.502 Chain C: V.453, E.456, N.457, E.486, W.491, S.492, T.493, Y.494, D.498, F.632, F.635, K.636, S.662 Ligands: AMP.9, POP.10 16 PLIP interactions: 3 interactions with chain B, 13 interactions with chain C Hydrogen bonds: B:R.355, B:N.472, C:E.456, C:N.457, C:E.486, C:S.492, C:S.492, C:Y.494, C:S.662 Water bridges: B:R.469, C:R.628 Salt bridges: C:K.636, C:K.636 pi-Stacking: C:W.491, C:F.635, C:F.635 DND.12: 22 residues within 4Å: Chain A: R.355, L.359, A.471, N.472, G.476, I.477, H.502 Chain D: V.453, E.456, N.457, E.486, W.491, S.492, T.493, Y.494, D.498, F.632, F.635, K.636, S.662 Ligands: AMP.13, POP.14 15 PLIP interactions: 11 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:E.456, D:N.457, D:S.492, D:S.492, D:Y.494, D:S.662, A:R.355, A:N.472 Salt bridges: D:K.636, D:K.636 pi-Stacking: D:W.491, D:F.635, D:F.635 Water bridges: A:F.468, A:N.472 DND.16: 20 residues within 4Å: Chain E: V.453, E.456, N.457, 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: AMP.17 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain H Hydrogen bonds: E:E.456, E:N.457, E:S.492, E:Y.494, E:S.662, H:R.355, H:N.472 Salt bridges: E:K.636, E:K.636 pi-Stacking: E:F.635, E:F.635 DND.19: 21 residues within 4Å: Chain F: V.453, E.456, 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: AMP.20 16 PLIP interactions: 12 interactions with chain F, 4 interactions with chain G Hydrogen bonds: F:E.456, F:N.457, F:E.486, 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 Water bridges: G:F.468, G:R.469 DND.23: 22 residues within 4Å: Chain F: R.355, L.359, A.471, N.472, G.476, I.477, H.502 Chain G: V.453, E.456, N.457, E.486, W.491, S.492, T.493, Y.494, D.498, F.632, F.635, K.636, S.662 Ligands: AMP.24, POP.25 16 PLIP interactions: 13 interactions with chain G, 3 interactions with chain F Hydrogen bonds: G:E.456, G:N.457, G:E.486, G:S.492, G:S.492, G:Y.494, G:S.662, F:R.355, F:N.472 Water bridges: G:R.628, F:R.469 Salt bridges: G:K.636, G:K.636 pi-Stacking: G:W.491, G:F.635, G:F.635 DND.27: 22 residues within 4Å: Chain E: R.355, L.359, A.471, N.472, G.476, I.477, H.502 Chain H: V.453, E.456, N.457, E.486, W.491, S.492, T.493, Y.494, D.498, F.632, F.635, K.636, S.662 Ligands: AMP.28, POP.29 15 PLIP interactions: 11 interactions with chain H, 4 interactions with chain E Hydrogen bonds: H:E.456, H:N.457, H:S.492, H:S.492, H:Y.494, H:S.662, E:R.355, E:N.472 Salt bridges: H:K.636, H:K.636 pi-Stacking: H:W.491, H:F.635, H:F.635 Water bridges: E:F.468, E:N.472

8 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 12 residues within 4Å: Chain A: G.367, V.368, S.369, S.374, F.398, A.399, L.400, P.401, R.463, T.481 Ligands: DND.1, POP.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.374, A:S.374, A:L.400, A:R.463, A:T.481 pi-Cation interactions: A:R.463 AMP.5: 12 residues within 4Å: Chain B: G.367, V.368, S.369, S.374, F.398, A.399, L.400, P.401, R.463, T.481 Ligands: DND.4, POP.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.367, B:S.369, B:L.400, B:R.463 Water bridges: B:R.463 pi-Cation interactions: B:R.463 AMP.9: 12 residues within 4Å: Chain C: G.367, V.368, S.369, S.374, F.398, A.399, L.400, R.463, T.481, D.498 Ligands: DND.8, POP.10 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:L.400, C:R.463, C:T.481, C:T.481 Water bridges: C:G.367, C:R.463, C:R.463 AMP.13: 12 residues within 4Å: Chain D: G.367, V.368, S.369, S.374, F.398, A.399, L.400, P.401, R.463, T.481 Ligands: DND.12, POP.14 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:L.400, D:R.463, D:T.481, D:T.481 Water bridges: D:G.367 AMP.17: 12 residues within 4Å: Chain E: G.367, V.368, S.369, S.374, F.398, A.399, L.400, P.401, R.463, T.481 Ligands: DND.16, POP.18 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:S.374, E:S.374, E:L.400, E:R.463, E:T.481, E:T.481 pi-Cation interactions: E:R.463 AMP.20: 12 residues within 4Å: Chain F: G.367, V.368, S.369, S.374, F.398, A.399, L.400, P.401, R.463, T.481 Ligands: DND.19, POP.21 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:G.367, F:S.369, F:L.400, F:R.463, F:T.481 Water bridges: F:R.463, F:D.498 pi-Cation interactions: F:R.463 AMP.24: 12 residues within 4Å: Chain G: G.367, V.368, S.369, S.374, F.398, A.399, L.400, R.463, T.481, D.498 Ligands: DND.23, POP.25 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:L.400, G:R.463, G:T.481 Water bridges: G:G.367, G:R.463, G:R.463 AMP.28: 12 residues within 4Å: Chain H: G.367, V.368, S.369, S.374, F.398, A.399, L.400, P.401, R.463, T.481 Ligands: DND.27, POP.29 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:L.400, H:R.463, H:T.481 Water bridges: H:G.367

8 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.3: 6 residues within 4Å: Chain A: S.369, G.371, L.372, D.373, S.374 Ligands: AMP.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.369, A:G.371, A:G.371, A:D.373, A:S.374, A:E.542 Water bridges: A:L.372 POP.6: 6 residues within 4Å: Chain B: S.369, G.371, L.372, D.373, S.374 Ligands: AMP.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.369, B:G.371, B:G.371, B:D.373, B:S.374 Water bridges: B:L.372 POP.10: 7 residues within 4Å: Chain C: S.369, G.371, L.372, D.373, S.374 Ligands: DND.8, AMP.9 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.369, C:G.371, C:D.373, C:D.373, C:S.374 Water bridges: C:E.542 POP.14: 7 residues within 4Å: Chain D: S.369, G.371, L.372, D.373, S.374 Ligands: DND.12, AMP.13 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.369, D:G.371, D:G.371, D:D.373, D:D.373, D:S.374 POP.18: 6 residues within 4Å: Chain E: S.369, G.371, L.372, D.373, S.374 Ligands: AMP.17 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:S.369, E:G.371, E:G.371, E:D.373, E:S.374, E:E.542, E:E.542 Water bridges: E:L.372 POP.21: 6 residues within 4Å: Chain F: S.369, G.371, L.372, D.373, S.374 Ligands: AMP.20 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:S.369, F:G.371, F:G.371, F:D.373, F:S.374 Water bridges: F:L.372, F:D.373, F:D.373 POP.25: 7 residues within 4Å: Chain G: S.369, G.371, L.372, D.373, S.374 Ligands: DND.23, AMP.24 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:S.369, G:G.371, G:D.373, G:S.374 POP.29: 7 residues within 4Å: Chain H: S.369, G.371, L.372, D.373, S.374 Ligands: DND.27, AMP.28 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:S.369, H:G.371, H:G.371, H:D.373, H:S.374

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain B: R.286, L.576, D.657 Chain D: Y.128, R.129 Chain G: D.63, L.66, R.135 6 PLIP interactions: 4 interactions with chain B, 1 interactions with chain G, 1 interactions with chain D Hydrogen bonds: B:R.286, B:L.576, B:D.657, G:R.135, D:R.129 Water bridges: B:R.286 GOL.11: 10 residues within 4Å: Chain C: Y.59, S.60, I.61, E.62, L.65, E.130, F.131, Y.132, E.133, Q.136 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.59, C:E.62, C:E.130, C:Y.132, C:Q.136, C:Q.136 GOL.15: 9 residues within 4Å: Chain D: Y.59, S.60, I.61, E.62, E.130, F.131, Y.132, E.133, Q.136 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Y.59, D:Y.59, D:E.62, D:E.130, D:Y.132, D:Y.132 GOL.22: 8 residues within 4Å: Chain C: D.63, L.66, R.135 Chain F: R.286, L.576, D.657 Chain H: Y.128, R.129 6 PLIP interactions: 1 interactions with chain C, 4 interactions with chain F, 1 interactions with chain H Hydrogen bonds: C:R.135, F:R.286, F:L.576, F:D.657, H:R.129 Water bridges: F:R.286 GOL.26: 10 residues within 4Å: Chain G: Y.59, S.60, I.61, E.62, L.65, E.130, F.131, Y.132, E.133, Q.136 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:E.62, G:E.130, G:Y.132, G:Q.136, G:Q.136 GOL.30: 9 residues within 4Å: Chain H: Y.59, S.60, I.61, E.62, E.130, F.131, Y.132, E.133, Q.136 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:Y.59, H:E.62, H:E.130, H:Y.132, H:Y.132

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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