SMTL ID : 3gwc.2 (1 other biounit)

Crystal structure of Mycobacterium tuberculosis thymidylate synthase X bound to FdUMP and FAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 23 residues within 4Å: Chain A: R.95, H.96, R.97, H.98, H.194, M.198, R.199, H.203 Chain B: C.43, S.71, E.74, H.98, N.188, R.190 Chain D: S.100, Y.101, S.102, Q.103, S.105, R.107, Y.108 Ligands: FAD.3, UFP.8 27 PLIP interactions: 14 interactions with chain A, 10 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: A:H.203 Hydrogen bonds: A:R.95, A:R.95, A:R.97, A:R.97, A:H.194, B:S.71, B:S.71, B:N.188, B:R.190, B:R.190, D:S.100, D:Q.103, D:Q.103 Water bridges: A:H.98, A:F.99, B:S.71, B:R.190 Salt bridges: A:H.96, A:H.96, A:R.97, A:R.97, A:H.194, A:H.194, B:R.190 pi-Stacking: B:H.98, B:H.98 FAD.3: 23 residues within 4Å: Chain A: C.43, S.71, E.74, H.98, N.188, R.190, A.191 Chain B: R.95, H.96, R.97, H.98, H.194, M.198, R.199, H.203 Chain C: S.100, S.102, Q.103, S.105, R.107, Y.108 Ligands: FAD.1, UFP.6 27 PLIP interactions: 15 interactions with chain B, 3 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: B:H.203 Hydrogen bonds: B:R.95, B:R.95, B:R.97, B:R.97, B:H.194, B:R.199, C:S.100, C:Q.103, C:Q.103, A:S.71, A:S.71, A:H.98, A:N.188 Water bridges: B:H.96, B:H.98, A:S.71, A:S.71 Salt bridges: B:H.96, B:H.96, B:R.97, B:R.97, B:H.194, B:H.194, A:R.190 pi-Stacking: A:H.98, A:H.98 FAD.5: 21 residues within 4Å: Chain B: S.100, S.102, Q.103, S.105, Y.108 Chain C: R.95, H.96, R.97, H.98, H.194, M.198, R.199, H.203 Chain D: C.43, S.71, E.74, H.98, N.188, R.190 Ligands: UFP.4, FAD.7 27 PLIP interactions: 16 interactions with chain C, 8 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: C:H.203 Hydrogen bonds: C:R.95, C:R.95, C:R.97, C:R.97, C:H.194, D:S.71, D:N.188, B:S.100, B:Q.103, B:Q.103 Water bridges: C:R.95, C:H.96, C:R.97, C:H.98, D:S.71, D:S.71, D:R.190 Salt bridges: C:H.96, C:H.96, C:R.97, C:R.97, C:H.194, C:H.194, D:R.190 pi-Stacking: D:H.98, D:H.98 FAD.7: 23 residues within 4Å: Chain A: S.100, S.102, Q.103, S.105, R.107, Y.108 Chain C: C.43, S.71, E.74, H.98, N.188, R.190, A.191 Chain D: R.95, H.96, R.97, H.98, H.194, M.198, R.199, H.203 Ligands: UFP.2, FAD.5 30 PLIP interactions: 5 interactions with chain A, 10 interactions with chain C, 15 interactions with chain D Hydrogen bonds: A:S.100, A:Q.103, A:Q.103, A:S.105, C:S.71, C:S.71, C:H.98, C:N.188, D:R.95, D:R.95, D:R.97, D:R.97, D:H.194, D:R.199 Water bridges: A:Y.108, C:S.71, C:R.190, C:R.190, D:H.98, D:H.98 Salt bridges: C:R.190, D:H.96, D:H.96, D:R.97, D:R.97, D:H.194, D:H.194 pi-Stacking: C:H.98, C:H.98 Hydrophobic interactions: D:H.203

4 x UFP: 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE(Non-covalent)

UFP.2: 13 residues within 4Å: Chain A: R.87, Q.103, L.104, S.105, Q.106, R.107, Y.108, R.172 Chain D: H.91, E.92, R.95, R.199 Ligands: FAD.7 16 PLIP interactions: 6 interactions with chain A, 10 interactions with chain D Hydrogen bonds: A:Q.106, A:R.107, A:R.107, D:H.91, D:H.91, D:E.92, D:E.92, D:E.92, D:R.95, D:R.199, D:R.199 Water bridges: A:R.87, D:E.92 Salt bridges: A:R.87, A:R.172 Hydrophobic interactions: D:R.95 UFP.4: 13 residues within 4Å: Chain B: R.87, Q.103, L.104, S.105, Q.106, R.107, Y.108, R.172 Chain C: H.91, E.92, R.95, R.199 Ligands: FAD.5 15 PLIP interactions: 7 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:Q.106, B:R.107, B:R.107, C:H.91, C:H.91, C:E.92, C:E.92, C:R.95, C:R.199, C:R.199 Water bridges: B:R.87, B:R.87 Salt bridges: B:R.87, B:R.172 Hydrophobic interactions: C:R.95 UFP.6: 13 residues within 4Å: Chain B: H.91, E.92, R.95, R.199 Chain C: R.87, Q.103, L.104, S.105, Q.106, R.107, Y.108, R.172 Ligands: FAD.3 16 PLIP interactions: 9 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:R.95 Hydrogen bonds: B:H.91, B:E.92, B:E.92, B:R.95, B:R.199, B:R.199, C:Q.106, C:R.107, C:R.107 Water bridges: B:E.92, B:E.92, C:R.87, C:R.172 Salt bridges: C:R.87, C:R.172 UFP.8: 13 residues within 4Å: Chain A: H.91, E.92, R.95, R.199 Chain D: R.87, Q.103, L.104, S.105, Q.106, R.107, Y.108, R.172 Ligands: FAD.1 14 PLIP interactions: 7 interactions with chain D, 7 interactions with chain A Hydrogen bonds: D:Q.106, D:R.107, D:R.107, A:H.91, A:E.92, A:E.92, A:R.95, A:R.199, A:R.199 Water bridges: D:R.87, D:R.87 Salt bridges: D:R.87, D:R.172 Hydrophobic interactions: A:R.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baugh, L. et al., Increasing the structural coverage of tuberculosis drug targets. Tuberculosis (Edinb) (2015)

Release Date

2009-04-28

Peptides

Thymidylate synthase thyX: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Thymidylate synthase thyX

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