SMTL ID : 3dla.1

X-ray crystal structure of glutamine-dependent NAD+ synthetase from Mycobacterium tuberculosis bound to NaAD+ and DON

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-octamer

Ligands

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

DND.1: 18 residues within 4Å: Chain A: 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 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:N.457, A:W.491, A:S.492, A:S.492, A:Y.494, A:S.662, D:R.355, D:N.472, D:N.472, D:H.502 Water bridges: A:F.635, D:N.472 Salt bridges: A:K.636, A:K.636 pi-Stacking: A:F.635, A:F.635 DND.8: 19 residues within 4Å: Chain B: N.457, A.460, 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 20 PLIP interactions: 14 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:A.460, B:D.498 Hydrogen bonds: B:W.491, B:S.492, B:S.492, B:Y.494, B:S.662, C:R.355, C:N.472, C:N.472, C:H.502 Water bridges: B:R.628, B:F.635, C:R.469, C:N.472 Salt bridges: B:K.636, B:K.636 pi-Stacking: B:W.491, B:F.635, B:F.635 DND.13: 20 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 20 PLIP interactions: 14 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:E.456, C:N.457, C:N.457, C:E.486, C:S.492, C:S.492, C:Y.494, C:S.662, B:R.355, B:N.472, B:N.472 Water bridges: C:F.635, B:N.472, B:N.472, B:N.472 Salt bridges: C:K.636, C:K.636 pi-Stacking: C:W.491, C:F.635, C:F.635 DND.18: 19 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, W.491, S.492, T.493, Y.494, D.498, F.632, F.635, K.636, S.662 17 PLIP interactions: 13 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:E.456, D:N.457, D:N.457, D:S.492, D:S.492, D:Y.494, D:S.662, A:R.355, A:N.472 Water bridges: D:R.628, D:F.635, A:N.472, A:G.476 Salt bridges: D:K.636, D:K.636 pi-Stacking: D:F.635, D:F.635 DND.24: 18 residues within 4Å: Chain E: 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 15 PLIP interactions: 4 interactions with chain H, 11 interactions with chain E Hydrogen bonds: H:R.355, H:N.472, H:N.472, E:N.457, E:W.491, E:S.492, E:S.492, E:Y.494, E:S.662 Water bridges: H:N.472, E:F.635 Salt bridges: E:K.636, E:K.636 pi-Stacking: E:F.635, E:F.635 DND.31: 19 residues within 4Å: Chain F: N.457, A.460, 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 19 PLIP interactions: 14 interactions with chain F, 5 interactions with chain G Hydrophobic interactions: F:A.460, F:D.498 Hydrogen bonds: F:W.491, F:S.492, F:S.492, F:Y.494, F:S.662, G:R.355, G:N.472, G:N.472 Water bridges: F:R.628, F:F.635, G:R.469, G:N.472 Salt bridges: F:K.636, F:K.636 pi-Stacking: F:W.491, F:F.635, F:F.635 DND.36: 20 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 21 PLIP interactions: 7 interactions with chain F, 14 interactions with chain G Hydrogen bonds: F:R.355, F:N.472, F:N.472, F:H.502, G:E.456, G:N.457, G:N.457, G:E.486, G:S.492, G:S.492, G:Y.494, G:S.662 Water bridges: F:N.472, F:N.472, F:N.472, G:F.635 Salt bridges: G:K.636, G:K.636 pi-Stacking: G:W.491, G:F.635, G:F.635 DND.41: 19 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, W.491, S.492, T.493, Y.494, D.498, F.632, F.635, K.636, S.662 18 PLIP interactions: 13 interactions with chain H, 5 interactions with chain E Hydrogen bonds: H:E.456, H:N.457, H:N.457, H:S.492, H:S.492, H:Y.494, H:S.662, E:R.355, E:N.472, E:H.502 Water bridges: H:R.628, H:F.635, E:N.472, E:G.476 Salt bridges: H:K.636, H:K.636 pi-Stacking: H:F.635, H:F.635

8 x ONL: 5-OXO-L-NORLEUCINE(Covalent)

ONL.2: 9 residues within 4Å: Chain B: F.131, C.177, M.180, F.181, S.202, S.204, R.210, R.214, Y.231 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.181, B:F.181, B:R.210, B:R.214 Hydrogen bonds: B:S.202, B:Y.231 Water bridges: B:E.178 Salt bridges: B:R.210 ONL.3: 9 residues within 4Å: Chain C: K.122, P.126, Y.128, F.131, E.133, C.177, E.178, F.181, R.210 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.131, C:F.181 Hydrogen bonds: C:K.122, C:E.178, C:R.210 Water bridges: C:R.129 Salt bridges: C:R.210 ONL.4: 8 residues within 4Å: Chain D: P.126, Y.128, F.131, C.177, E.178, F.181, S.204, R.210 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.131 Hydrogen bonds: D:E.178 Water bridges: D:R.210, D:R.210 Salt bridges: D:R.210 ONL.5: 7 residues within 4Å: Chain A: K.122, P.126, Y.128, F.131, C.177, E.178, F.181 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.131, A:F.181 Hydrogen bonds: A:K.122, A:Y.128, A:Y.128, A:E.178, A:E.178 Water bridges: A:R.210 Salt bridges: A:R.210 ONL.25: 9 residues within 4Å: Chain F: F.131, C.177, M.180, F.181, S.202, S.204, R.210, R.214, Y.231 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:F.181, F:F.181, F:R.210, F:R.214 Hydrogen bonds: F:S.202 Water bridges: F:E.178 Salt bridges: F:R.210 ONL.26: 9 residues within 4Å: Chain G: K.122, P.126, Y.128, F.131, E.133, C.177, E.178, F.181, R.210 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:F.131, G:F.181 Hydrogen bonds: G:K.122, G:Y.128, G:E.178, G:E.178, G:R.210 Water bridges: G:R.129 Salt bridges: G:R.210 ONL.27: 8 residues within 4Å: Chain H: P.126, Y.128, F.131, C.177, E.178, F.181, S.204, R.210 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:F.131 Hydrogen bonds: H:Y.128, H:E.178, H:E.178 Water bridges: H:R.210, H:R.210 Salt bridges: H:R.210 ONL.28: 7 residues within 4Å: Chain E: K.122, P.126, Y.128, F.131, C.177, E.178, F.181 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:F.131, E:F.181 Hydrogen bonds: E:K.122, E:Y.128, E:E.178 Water bridges: E:R.210 Salt bridges: E:R.210

30 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 1 residues within 4Å: Chain A: T.146 Ligand excluded by PLIP GOL.7: 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 Ligand excluded by PLIP GOL.9: 7 residues within 4Å: Chain B: G.367, V.368, S.369, F.398, A.399, L.400, R.463 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain B: R.99, H.100, R.101, I.147, R.148 Ligand excluded by PLIP GOL.11: 8 residues within 4Å: Chain A: R.286, L.576, D.657 Chain B: D.63, L.66, R.135 Chain E: Y.128, R.129 Ligand excluded by PLIP GOL.12: 3 residues within 4Å: Chain B: V.268, R.269, R.270 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain C: R.286, L.576, D.657 Chain D: D.63, R.135 Chain G: R.129 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain C: A.28, A.73, D.76, A.77, D.80 Ligand excluded by PLIP GOL.16: 11 residues within 4Å: Chain C: L.125, P.126, T.127, Y.128 Chain G: R.286, G.288, T.289, D.292 Chain H: R.103, R.134, R.135 Ligand excluded by PLIP GOL.17: 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 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain B: R.129 Chain D: R.286, L.576, D.657 Chain E: D.63, L.66, R.135 Ligand excluded by PLIP GOL.20: 8 residues within 4Å: Chain A: D.292, R.295 Chain B: R.134, P.139, D.141 Chain D: D.292, R.295 Chain E: R.134 Ligand excluded by PLIP GOL.21: 3 residues within 4Å: Chain D: R.434, L.435, H.438 Ligand excluded by PLIP GOL.22: 10 residues within 4Å: Chain D: Y.59, S.60, I.61, E.62, L.65, E.130, F.131, Y.132, E.133, Q.136 Ligand excluded by PLIP GOL.23: 3 residues within 4Å: Chain D: V.268, R.269, R.270 Ligand excluded by PLIP GOL.29: 1 residues within 4Å: Chain E: T.146 Ligand excluded by PLIP GOL.30: 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 Ligand excluded by PLIP GOL.32: 7 residues within 4Å: Chain F: G.367, V.368, S.369, F.398, A.399, L.400, R.463 Ligand excluded by PLIP GOL.33: 5 residues within 4Å: Chain F: R.99, H.100, R.101, I.147, R.148 Ligand excluded by PLIP GOL.34: 8 residues within 4Å: Chain A: Y.128, R.129 Chain E: R.286, L.576, D.657 Chain F: D.63, L.66, R.135 Ligand excluded by PLIP GOL.35: 3 residues within 4Å: Chain F: V.268, R.269, R.270 Ligand excluded by PLIP GOL.37: 6 residues within 4Å: Chain C: R.129 Chain G: R.286, L.576, D.657 Chain H: D.63, R.135 Ligand excluded by PLIP GOL.38: 5 residues within 4Å: Chain G: A.28, A.73, D.76, A.77, D.80 Ligand excluded by PLIP GOL.39: 11 residues within 4Å: Chain C: R.286, G.288, T.289, D.292 Chain D: R.103, R.134, R.135 Chain G: L.125, P.126, T.127, Y.128 Ligand excluded by PLIP GOL.40: 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 Ligand excluded by PLIP GOL.42: 7 residues within 4Å: Chain A: D.63, L.66, R.135 Chain F: R.129 Chain H: R.286, L.576, D.657 Ligand excluded by PLIP GOL.43: 8 residues within 4Å: Chain A: R.134 Chain E: D.292, R.295 Chain F: R.134, P.139, D.141 Chain H: D.292, R.295 Ligand excluded by PLIP GOL.44: 3 residues within 4Å: Chain H: R.434, L.435, H.438 Ligand excluded by PLIP GOL.45: 10 residues within 4Å: Chain H: Y.59, S.60, I.61, E.62, L.65, E.130, F.131, Y.132, E.133, Q.136 Ligand excluded by PLIP GOL.46: 3 residues within 4Å: Chain H: V.268, R.269, R.270 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

LaRonde-LeBlanc, N. et al., Regulation of active site coupling in glutamine-dependent NAD(+) synthetase. Nat.Struct.Mol.Biol. (2009)

Release Date

2009-03-10

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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