SMTL ID : 6ofc.1

Crystal structure of M. tuberculosis glutamine-dependent NAD+ synthetase complexed with Sulfonamide derivative 1, pyrophosphate, and glutamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.14 Å

Oligo State

homo-octamer

Ligands

16 x SFH: 5'-O-[(pyridine-3-carbonyl)sulfamoyl]adenosine(Non-covalent)

SFH.1: 13 residues within 4Å: Chain A: G.366, V.367, S.368, S.373, F.397, A.398, L.399, R.462, T.480, W.490, S.491, T.492, D.497 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.366, A:S.373, A:S.373, A:L.399, A:R.462, A:T.480 Water bridges: A:S.368, A:G.370, A:E.553 pi-Stacking: A:W.490, A:W.490 SFH.2: 12 residues within 4Å: Chain A: N.456, T.492, Y.493, F.634, K.635, S.661 Chain D: R.354, L.358, N.471, G.475, I.476, H.501 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:N.456, A:S.491, A:Y.493, A:K.635, A:S.661, D:R.354, D:N.471 Salt bridges: A:K.635 pi-Stacking: A:F.634, A:F.634 SFH.3: 14 residues within 4Å: Chain A: R.354, L.358, N.471, G.475, I.476, H.501 Chain D: G.489, S.491, R.627, F.631, F.634, K.635, S.661 Ligands: SFH.15 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain D Hydrogen bonds: A:R.354, A:A.470, D:S.491, D:K.635, D:S.661 pi-Stacking: D:F.634, D:F.634 pi-Cation interactions: D:K.635 SFH.6: 15 residues within 4Å: Chain B: G.366, V.367, S.368, S.373, F.397, A.398, L.399, R.462, T.480, W.490, S.491, T.492, D.497, E.552 Ligands: POP.10 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.490 Hydrogen bonds: B:G.366, B:S.373, B:L.399, B:R.462, B:T.480, B:E.552 Water bridges: B:R.462 pi-Stacking: B:W.490 SFH.7: 13 residues within 4Å: Chain B: N.456, S.491, T.492, Y.493, F.631, F.634, K.635, S.661 Chain C: R.354, L.358, N.471, G.475, H.501 15 PLIP interactions: 3 interactions with chain C, 12 interactions with chain B Hydrogen bonds: C:R.354, C:N.471, C:G.475, B:N.456, B:S.491, B:S.491, B:T.492, B:Y.493, B:K.635, B:S.661 Water bridges: B:R.627 Salt bridges: B:K.635 pi-Stacking: B:F.631, B:F.634, B:F.634 SFH.8: 14 residues within 4Å: Chain B: R.354, L.358, N.471, G.475, I.476, H.501 Chain C: N.456, S.491, T.492, Y.493, R.627, F.634, K.635, S.661 11 PLIP interactions: 2 interactions with chain B, 9 interactions with chain C Hydrogen bonds: B:R.354, B:N.471, C:S.491, C:S.491, C:Y.493, C:R.627, C:K.635, C:S.661 Salt bridges: C:K.635 pi-Stacking: C:F.634, C:F.634 SFH.13: 13 residues within 4Å: Chain C: G.366, V.367, S.368, S.373, F.397, A.398, L.399, R.462, T.480, W.490, S.491, T.492, D.497 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:W.490 Hydrogen bonds: C:S.373, C:L.399, C:T.492 Water bridges: C:G.366, C:G.366, C:S.368, C:S.368 pi-Stacking: C:W.490 SFH.15: 14 residues within 4Å: Chain D: G.366, V.367, S.368, S.373, F.397, A.398, L.399, R.462, T.480, W.490, S.491, T.492, D.497 Ligands: SFH.3 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.366, D:L.399, D:R.462, D:T.492 Water bridges: D:S.373 pi-Stacking: D:W.490, D:W.490 SFH.19: 13 residues within 4Å: Chain E: G.366, V.367, S.368, S.373, F.397, A.398, L.399, R.462, T.480, W.490, S.491, T.492, D.497 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:G.366, E:S.373, E:S.373, E:L.399, E:R.462, E:T.492, E:D.497 Water bridges: E:S.368, E:G.370, E:E.553 pi-Stacking: E:W.490, E:W.490 SFH.20: 12 residues within 4Å: Chain E: N.456, T.492, Y.493, F.634, K.635, S.661 Chain H: R.354, L.358, N.471, G.475, I.476, H.501 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain H Hydrogen bonds: E:N.456, E:S.491, E:Y.493, E:K.635, E:S.661, H:R.354, H:N.471 Salt bridges: E:K.635 pi-Stacking: E:F.634, E:F.634 SFH.21: 14 residues within 4Å: Chain E: R.354, L.358, N.471, G.475, I.476, H.501 Chain H: G.489, S.491, R.627, F.631, F.634, K.635, S.661 Ligands: SFH.33 8 PLIP interactions: 6 interactions with chain H, 2 interactions with chain E Hydrogen bonds: H:S.491, H:K.635, H:S.661, E:R.354, E:A.470 pi-Stacking: H:F.634, H:F.634 pi-Cation interactions: H:K.635 SFH.24: 15 residues within 4Å: Chain F: G.366, V.367, S.368, S.373, F.397, A.398, L.399, R.462, T.480, W.490, S.491, T.492, D.497, E.552 Ligands: POP.28 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:W.490 Hydrogen bonds: F:G.366, F:S.373, F:L.399, F:R.462, F:T.492, F:E.552, F:E.552 Water bridges: F:R.462 pi-Stacking: F:W.490 SFH.25: 13 residues within 4Å: Chain F: N.456, S.491, T.492, Y.493, F.631, F.634, K.635, S.661 Chain G: R.354, L.358, N.471, G.475, H.501 15 PLIP interactions: 3 interactions with chain G, 12 interactions with chain F Hydrogen bonds: G:R.354, G:N.471, G:G.475, F:N.456, F:S.491, F:S.491, F:T.492, F:Y.493, F:K.635, F:S.661 Water bridges: F:R.627 Salt bridges: F:K.635 pi-Stacking: F:F.631, F:F.634, F:F.634 SFH.26: 14 residues within 4Å: Chain F: R.354, L.358, N.471, G.475, I.476, H.501 Chain G: N.456, S.491, T.492, Y.493, R.627, F.634, K.635, S.661 11 PLIP interactions: 9 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:S.491, G:S.491, G:Y.493, G:R.627, G:K.635, G:S.661, F:R.354, F:N.471 Salt bridges: G:K.635 pi-Stacking: G:F.634, G:F.634 SFH.31: 13 residues within 4Å: Chain G: G.366, V.367, S.368, S.373, F.397, A.398, L.399, R.462, T.480, W.490, S.491, T.492, D.497 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:W.490 Hydrogen bonds: G:S.373, G:L.399, G:T.480 Water bridges: G:G.366, G:G.366, G:D.372, G:D.372 pi-Stacking: G:W.490 SFH.33: 14 residues within 4Å: Chain H: G.366, V.367, S.368, S.373, F.397, A.398, L.399, R.462, T.480, W.490, S.491, T.492, D.497 Ligands: SFH.21 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:G.366, H:L.399, H:R.462, H:T.480 Water bridges: H:D.372 pi-Stacking: H:W.490, H:W.490

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: T.463, D.497 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: S.630, S.661, D.662, M.663 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: T.463, D.497, M.499 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain D: T.463, G.496, D.497, M.499 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain E: T.463, D.497 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain E: S.630, S.661, D.662, M.663 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain F: T.463, D.497, M.499 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain H: T.463, G.496, D.497, M.499 Ligand excluded by PLIP

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

POP.10: 10 residues within 4Å: Chain B: S.368, G.370, L.371, D.372, S.373, E.541, E.552, E.553, L.554 Ligands: SFH.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.368, B:S.368, B:G.370, B:G.370, B:D.372, B:D.372, B:S.373, B:E.553, B:E.553 POP.28: 10 residues within 4Å: Chain F: S.368, G.370, L.371, D.372, S.373, E.541, E.552, E.553, L.554 Ligands: SFH.24 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:S.368, F:S.368, F:G.370, F:G.370, F:D.372, F:S.373, F:E.552, F:E.553, F:E.553

6 x GLN: GLUTAMINE(Non-covalent)

GLN.11: 5 residues within 4Å: Chain B: R.218 Chain D: E.211, L.215, R.218, W.251 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:R.218, D:R.218, D:R.218 Salt bridges: B:R.218 GLN.14: 12 residues within 4Å: Chain C: E.52, Y.58, K.121, P.125, Y.127, F.130, E.132, A.176, E.177, F.180, S.203, R.209 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.130 Hydrogen bonds: C:E.52, C:K.121, C:E.177, C:S.203 Water bridges: C:G.202 Salt bridges: C:R.209 GLN.17: 7 residues within 4Å: Chain D: Y.127, F.130, E.177, F.180, S.201, S.203, R.209 8 PLIP interactions: 7 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:F.130, D:F.130 Hydrogen bonds: D:Y.127, D:E.177, D:S.201, D:S.201, Q.17 Salt bridges: D:R.209 GLN.29: 5 residues within 4Å: Chain F: R.218 Chain H: E.211, L.215, R.218, W.251 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain H Hydrogen bonds: F:R.218, H:R.218, H:R.218 Salt bridges: F:R.218 GLN.32: 12 residues within 4Å: Chain G: E.52, Y.58, K.121, P.125, Y.127, F.130, E.132, A.176, E.177, F.180, S.203, R.209 8 PLIP interactions: 8 interactions with chain G, Hydrophobic interactions: G:F.130 Hydrogen bonds: G:E.52, G:K.121, G:Y.127, G:E.177, G:S.203 Water bridges: G:G.202 Salt bridges: G:R.209 GLN.35: 7 residues within 4Å: Chain H: Y.127, F.130, E.177, F.180, S.201, S.203, R.209 7 PLIP interactions: 6 interactions with chain H, 1 Ligand-Ligand interactions Hydrophobic interactions: H:F.130, H:F.130 Hydrogen bonds: H:E.177, H:S.201, H:S.201, Q.35 Salt bridges: H:R.209

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 8 residues within 4Å: Chain A: R.285, L.575, D.656 Chain B: D.62, L.65, R.134 Chain E: Y.127, R.128 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 1 interactions with chain E Hydrogen bonds: A:R.285, A:L.575, B:D.62, B:R.134, E:R.128 GOL.18: 7 residues within 4Å: Chain B: R.128 Chain D: R.285, L.575, D.656 Chain E: D.62, L.65, R.134 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:R.285, D:L.575, B:R.128 GOL.30: 8 residues within 4Å: Chain A: Y.127, R.128 Chain E: R.285, L.575, D.656 Chain F: D.62, L.65, R.134 5 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: F:D.62, F:R.134, E:R.285, E:L.575, A:R.128 GOL.36: 7 residues within 4Å: Chain A: D.62, L.65, R.134 Chain F: R.128 Chain H: R.285, L.575, D.656 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain F Hydrogen bonds: H:R.285, H:L.575, F:R.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chuenchor, W. et al., Different ways to transport ammonia in human and Mycobacterium tuberculosis NAD+synthetases. Nat Commun (2020)

Release Date

2020-01-08

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