SMTL ID : 3hzg.1 (4 other biounits)

Crystal structure of mycobacterium tuberculosis thymidylate synthase X bound with FAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-tetramer

Ligands

9 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 8 residues within 4Å: Chain A: R.87, Q.103, S.105, Q.106, R.172 Chain D: H.91, E.92 Ligands: PO4.14 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:S.105, A:Q.106, A:R.107, D:E.92 Water bridges: A:R.87, A:Q.103, A:R.172, D:H.91 Salt bridges: A:R.87, A:R.172 PO4.2: 6 residues within 4Å: Chain A: E.92, R.95, R.199 Chain D: R.107 Ligands: FAD.8, PO4.15 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:R.95, D:R.107 Salt bridges: A:R.199 PO4.5: 6 residues within 4Å: Chain B: R.87, S.105, Q.106, R.172 Chain C: E.92 Ligands: PO4.9 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.103, B:Q.106, C:E.92 Water bridges: B:R.87, B:R.87 Salt bridges: B:R.87, B:R.172 PO4.6: 5 residues within 4Å: Chain B: E.92, R.95, R.199 Ligands: FAD.3, PO4.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.92 Salt bridges: B:R.95, B:R.199 PO4.7: 8 residues within 4Å: Chain B: R.87, S.88, H.91, N.177 Chain C: R.87, S.88, H.91, N.177 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.87, B:N.177 Salt bridges: B:H.91, C:R.87, C:H.91 PO4.9: 6 residues within 4Å: Chain C: E.92, R.95, R.199 Ligands: PO4.5, FAD.11, GOL.13 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Water bridges: B:Q.103, C:R.199 Hydrogen bonds: C:E.92 Salt bridges: C:R.95, C:R.199 PO4.10: 8 residues within 4Å: Chain B: E.92 Chain C: R.87, Q.103, S.105, Q.106, R.107, R.172 Ligands: PO4.6 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.103, C:Q.106, C:R.107 Water bridges: C:R.87, C:R.172 Salt bridges: C:R.87, C:R.172 PO4.14: 5 residues within 4Å: Chain D: E.92, R.95, R.199 Ligands: PO4.1, FAD.16 6 PLIP interactions: 6 interactions with chain D Water bridges: D:R.95, D:R.95, D:R.95, D:R.95 Salt bridges: D:R.95, D:R.199 PO4.15: 7 residues within 4Å: Chain A: H.91, E.92 Chain D: R.87, S.105, Q.106, R.172 Ligands: PO4.2 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.106 Salt bridges: D:R.87, D:R.172

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

FAD.3: 21 residues within 4Å: Chain A: C.43, Y.44, G.68, H.69, S.71, E.74, H.98, N.188, R.190 Chain B: R.95, H.96, R.97, H.98, H.194, R.199 Chain C: S.102, Q.103, S.105, Y.108 Ligands: PO4.6, FAD.8 29 PLIP interactions: 15 interactions with chain B, 11 interactions with chain A, 3 interactions with chain C Hydrogen bonds: B:R.95, B:R.95, B:R.97, B:R.97, B:H.194, B:R.199, B:R.199, B:R.199, A:S.71, A:N.188, A:R.190, A:R.190, C:Q.103, C:Q.103 Water bridges: B:H.98, B:H.98, A:H.98, A:R.190, C:R.97 Salt bridges: B:H.96, B:H.96, B:R.97, B:H.194, B:H.194, A:R.190 pi-Stacking: A:H.69, A:H.69, A:H.98, A:H.98 FAD.8: 22 residues within 4Å: Chain A: R.95, H.96, R.97, H.98, H.194, R.199 Chain B: C.43, Y.44, G.68, H.69, S.71, E.74, H.98, N.188, R.190, A.191 Chain D: S.100, S.102, Q.103, S.105 Ligands: PO4.2, FAD.3 28 PLIP interactions: 11 interactions with chain B, 14 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: B:H.69 Hydrogen bonds: B:S.71, B:S.71, B:N.188, B:R.190, A:R.95, A:R.95, A:R.97, A:R.97, A:R.199, D:Q.103, D:Q.103 Water bridges: B:R.190, A:H.98, A:H.98, A:R.199, D:H.98 Salt bridges: B:R.190, A:H.96, A:H.96, A:R.97, A:R.97, A:H.194, A:H.194 pi-Stacking: B:H.69, B:H.69, B:H.98, B:H.98 FAD.11: 25 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 Chain D: C.43, Y.44, V.67, G.68, H.69, S.71, E.74, H.98, N.188, R.190 Ligands: PO4.9, GOL.13, FAD.16 32 PLIP interactions: 15 interactions with chain C, 13 interactions with chain D, 4 interactions with chain B Hydrogen bonds: C:R.95, C:R.95, C:R.97, C:R.97, C:H.194, C:R.199, C:R.199, D:S.71, D:S.71, D:N.188, D:R.190, D:R.190, B:S.100, B:Q.103, B:Q.103 Water bridges: C:H.96, C:H.98, D:H.98, B:Q.103 Salt bridges: C:H.96, C:H.96, C:R.97, C:R.97, C:H.194, C:H.194, D:R.190 Hydrophobic interactions: D:V.67, D:H.69 pi-Stacking: D:H.69, D:H.69, D:H.98, D:H.98 FAD.16: 25 residues within 4Å: Chain A: S.100, S.102, Q.103, S.105, Y.108 Chain C: C.43, Y.44, V.67, G.68, H.69, S.71, E.74, H.98, N.188, R.190, A.191 Chain D: R.95, H.96, R.97, H.98, H.194, R.199 Ligands: FAD.11, GOL.12, PO4.14 32 PLIP interactions: 13 interactions with chain C, 3 interactions with chain A, 16 interactions with chain D Hydrophobic interactions: C:H.69 Hydrogen bonds: C:S.71, C:S.71, C:N.188, C:R.190, C:R.190, A:S.100, A:Q.103, A:Q.103, D:R.95, D:R.95, D:R.97, D:R.97, D:H.194, D:R.199, D:R.199, D:R.199 Water bridges: C:S.71, C:H.98, 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.69, C:H.69, C:H.98, C:H.98

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: R.87, S.88, H.91, N.177 Chain D: R.87, H.91, N.177 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:R.87, D:R.87, D:N.177, A:R.87, A:R.87 Water bridges: D:N.177 GOL.12: 4 residues within 4Å: Chain C: F.70, R.190, R.193 Ligands: FAD.16 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.190, C:R.193 GOL.13: 8 residues within 4Å: Chain B: R.107, Y.108 Chain C: M.198, R.199, H.203, A.204 Ligands: PO4.9, FAD.11 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.107, B:Y.108, C:M.198, C:R.199 Water bridges: B:Y.108

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

2009-07-07

Peptides

Thymidylate synthase thyX: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Thymidylate synthase thyX

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