SMTL ID : 3syt.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-octamer

Ligands

8 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 8 residues within 4Å: Chain A: Y.128, R.129, F.131, C.177, E.178, F.181, S.204, R.210 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:F.181 Hydrogen bonds: A:E.178 Water bridges: A:E.178, A:S.204, A:S.204 Salt bridges: A:R.129, A:R.210, A:R.210 GLU.6: 8 residues within 4Å: Chain B: Y.128, R.129, F.131, C.177, E.178, F.181, S.204, R.210 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:F.181 Hydrogen bonds: B:E.178, B:E.178 Water bridges: B:E.178 Salt bridges: B:R.129, B:R.210, B:R.210 GLU.10: 9 residues within 4Å: Chain C: Y.128, R.129, F.131, C.177, E.178, F.181, S.204, R.210 Chain G: M.287 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:F.181 Hydrogen bonds: C:Y.128, C:E.178, C:E.178 Water bridges: C:E.178 Salt bridges: C:R.129, C:R.210, C:R.210 GLU.15: 8 residues within 4Å: Chain D: Y.128, R.129, F.131, C.177, E.178, F.181, S.204, R.210 11 PLIP interactions: 10 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:F.181 Hydrogen bonds: D:Y.128, D:R.129, D:E.178 Water bridges: D:E.178, D:E.178, D:S.204, D:S.204, E.15 Salt bridges: D:R.210, D:R.210 GLU.19: 8 residues within 4Å: Chain E: Y.128, R.129, F.131, C.177, E.178, F.181, S.204, R.210 9 PLIP interactions: 9 interactions with chain E, Hydrophobic interactions: E:F.181 Hydrogen bonds: E:Y.128, E:E.178 Water bridges: E:E.178, E:S.204, E:S.204 Salt bridges: E:R.129, E:R.210, E:R.210 GLU.24: 8 residues within 4Å: Chain F: Y.128, R.129, F.131, C.177, E.178, F.181, S.204, R.210 9 PLIP interactions: 9 interactions with chain F, Hydrophobic interactions: F:F.181 Hydrogen bonds: F:Y.128, F:E.178, F:E.178, F:E.178 Water bridges: F:E.178 Salt bridges: F:R.129, F:R.210, F:R.210 GLU.28: 9 residues within 4Å: Chain C: M.287 Chain G: Y.128, R.129, F.131, C.177, E.178, F.181, S.204, R.210 6 PLIP interactions: 6 interactions with chain G, Hydrophobic interactions: G:F.181 Hydrogen bonds: G:E.178 Water bridges: G:E.178 Salt bridges: G:R.129, G:R.210, G:R.210 GLU.33: 8 residues within 4Å: Chain H: Y.128, R.129, F.131, C.177, E.178, F.181, S.204, R.210 9 PLIP interactions: 1 Ligand-Ligand interactions, 8 interactions with chain H Water bridges: E.33, H:E.178, H:S.204, H:S.204 Hydrophobic interactions: H:F.181 Hydrogen bonds: H:R.129, H:E.178 Salt bridges: H:R.210, H:R.210

8 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 19 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, N.472, G.476, I.477, H.502 Ligands: AMP.3 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:N.457, A:N.457, A:E.486, A:Y.494, A:S.662, D:R.355, D:N.472 Water bridges: A:F.635, D:R.469, D:R.469, D:N.472 Salt bridges: A:K.636, A:K.636 pi-Stacking: A:W.491, A:F.635, A:F.635 NAD.7: 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: AMP.8 14 PLIP interactions: 3 interactions with chain C, 11 interactions with chain B Hydrogen bonds: C:R.355, C:N.472, B:N.457, B:E.486, B:S.492, B:Y.494, B:S.662 Water bridges: C:H.502, B:R.628 Salt bridges: B:K.636, B:K.636 pi-Stacking: B:W.491, B:F.635, B:F.635 NAD.12: 19 residues within 4Å: Chain B: R.355, L.359, N.472, G.476, I.477, H.502 Chain C: V.453, 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 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:N.457, C:E.486, C:Y.494, C:S.662, B:R.355, B:N.472 Water bridges: C:F.635 Salt bridges: C:K.636, C:K.636 pi-Stacking: C:W.491, C:F.635, C:F.635 NAD.16: 20 residues within 4Å: Chain A: R.355, L.359, A.471, N.472, G.476, I.477, H.502 Chain D: V.453, N.457, E.486, W.491, S.492, T.493, Y.494, D.498, F.632, F.635, K.636, S.662 Ligands: AMP.17 15 PLIP interactions: 10 interactions with chain D, 5 interactions with chain A Hydrogen bonds: D:N.457, D:E.486, D:Y.494, D:S.662, A:R.355, A:N.472 Water bridges: D:F.635, A:N.472, A:N.472, A:H.502 Salt bridges: D:K.636, D:K.636 pi-Stacking: D:W.491, D:F.635, D:F.635 NAD.20: 19 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, N.472, G.476, I.477, H.502 Ligands: AMP.21 16 PLIP interactions: 11 interactions with chain E, 5 interactions with chain H Hydrogen bonds: E:N.457, E:N.457, E:E.486, E:Y.494, E:S.662, H:R.355, H:N.472 Water bridges: E:F.635, H:R.469, H:R.469, H:N.472 Salt bridges: E:K.636, E:K.636 pi-Stacking: E:W.491, E:F.635, E:F.635 NAD.25: 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: AMP.26 14 PLIP interactions: 11 interactions with chain F, 3 interactions with chain G Hydrogen bonds: F:N.457, F:E.486, F:S.492, F:Y.494, F:S.662, G:R.355, G:N.472 Water bridges: F:R.628, G:H.502 Salt bridges: F:K.636, F:K.636 pi-Stacking: F:W.491, F:F.635, F:F.635 NAD.30: 19 residues within 4Å: Chain F: R.355, L.359, N.472, G.476, I.477, H.502 Chain G: V.453, N.457, E.486, W.491, S.492, T.493, Y.494, D.498, F.632, F.635, K.636, S.662 Ligands: AMP.31 12 PLIP interactions: 10 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:N.457, G:E.486, G:Y.494, G:S.662, F:R.355, F:N.472 Water bridges: G:F.635 Salt bridges: G:K.636, G:K.636 pi-Stacking: G:W.491, G:F.635, G:F.635 NAD.34: 20 residues within 4Å: Chain E: R.355, L.359, A.471, N.472, G.476, I.477, H.502 Chain H: V.453, N.457, E.486, W.491, S.492, T.493, Y.494, D.498, F.632, F.635, K.636, S.662 Ligands: AMP.35 15 PLIP interactions: 5 interactions with chain E, 10 interactions with chain H Hydrogen bonds: E:R.355, E:N.472, H:N.457, H:E.486, H:Y.494, H:S.662 Water bridges: E:N.472, E:N.472, E:H.502, H:F.635 Salt bridges: H:K.636, H:K.636 pi-Stacking: H:W.491, H:F.635, H:F.635

8 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 11 residues within 4Å: Chain A: G.367, V.368, S.369, S.374, F.398, A.399, L.400, R.463, T.481 Ligands: NAD.2, POP.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.400, A:R.463, A:T.481 Water bridges: A:G.367 AMP.8: 12 residues within 4Å: Chain B: G.367, V.368, S.369, S.374, F.398, A.399, L.400, R.463, T.481, D.498 Ligands: NAD.7, POP.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.400, B:T.481 AMP.13: 11 residues within 4Å: Chain C: G.367, V.368, S.369, S.374, F.398, A.399, L.400, R.463, T.481 Ligands: NAD.12, POP.14 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.400, C:R.463, C:T.481, C:T.481 AMP.17: 12 residues within 4Å: Chain D: G.367, V.368, S.369, S.374, F.398, A.399, L.400, R.463, T.481, D.498 Ligands: NAD.16, POP.18 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.21: 11 residues within 4Å: Chain E: G.367, V.368, S.369, S.374, F.398, A.399, L.400, R.463, T.481 Ligands: NAD.20, POP.22 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:L.400, E:R.463, E:T.481, E:T.481 Water bridges: E:G.367 AMP.26: 12 residues within 4Å: Chain F: G.367, V.368, S.369, S.374, F.398, A.399, L.400, R.463, T.481, D.498 Ligands: NAD.25, POP.27 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:L.400, F:T.481, F:T.481 AMP.31: 11 residues within 4Å: Chain G: G.367, V.368, S.369, S.374, F.398, A.399, L.400, R.463, T.481 Ligands: NAD.30, POP.32 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:L.400, G:R.463, G:T.481 AMP.35: 12 residues within 4Å: Chain H: G.367, V.368, S.369, S.374, F.398, A.399, L.400, R.463, T.481, D.498 Ligands: NAD.34, POP.36 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.4: 6 residues within 4Å: Chain A: S.369, G.371, L.372, D.373, S.374 Ligands: AMP.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.369, A:G.371, A:G.371, A:D.373, A:S.374, A:T.481 Water bridges: A:L.372, A:L.372, A:D.373 POP.9: 6 residues within 4Å: Chain B: S.369, G.371, L.372, D.373, S.374 Ligands: AMP.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.369, B:G.371, B:G.371, B:L.372, B:D.373, B:S.374 POP.14: 7 residues within 4Å: Chain C: S.369, G.371, L.372, D.373, S.374, T.481 Ligands: AMP.13 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.369, C:G.371, C:D.373, C:S.374, C:T.481 POP.18: 6 residues within 4Å: Chain D: S.369, G.371, L.372, D.373, S.374 Ligands: AMP.17 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.369, D:G.371, D:G.371, D:L.372, D:D.373, D:S.374 POP.22: 6 residues within 4Å: Chain E: S.369, G.371, L.372, D.373, S.374 Ligands: AMP.21 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:S.369, E:G.371, E:G.371, E:D.373, E:S.374, E:T.481, E:E.542 Water bridges: E:L.372, E:L.372, E:D.373, E:D.373 POP.27: 6 residues within 4Å: Chain F: S.369, G.371, L.372, D.373, S.374 Ligands: AMP.26 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:S.369, F:G.371, F:G.371, F:L.372, F:D.373, F:S.374 POP.32: 7 residues within 4Å: Chain G: S.369, G.371, L.372, D.373, S.374, T.481 Ligands: AMP.31 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:S.369, G:G.371, G:D.373, G:S.374 POP.36: 6 residues within 4Å: Chain H: S.369, G.371, L.372, D.373, S.374 Ligands: AMP.35 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:S.369, H:G.371, H:G.371, H:L.372, H:D.373, H:S.374

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 10 residues within 4Å: Chain A: 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 A Hydrogen bonds: A:S.60, A:E.62, A:E.130, A:Y.132, A:Q.136, A:Q.136 GOL.11: 9 residues within 4Å: Chain C: 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 C Hydrogen bonds: C:Y.59, C:S.60, C:E.62, C:Y.132, C:Q.136, C:Q.136 GOL.23: 10 residues within 4Å: Chain E: Y.59, S.60, I.61, E.62, L.65, E.130, F.131, Y.132, E.133, Q.136 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:Y.59, E:S.60, E:E.62, E:E.130, E:Y.132, E:Q.136, E:Q.136 GOL.29: 9 residues within 4Å: Chain G: Y.59, S.60, I.61, E.62, L.65, F.131, Y.132, E.133, Q.136 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:S.60, G:E.62, G:Y.132, G:Q.136, G:Q.136

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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