SMTL ID : 5chp.1

T. maritima ThyX in complex with TyC5-03

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 21 residues within 4Å: Chain A: R.92, H.93, R.94, I.95, N.183, L.187, R.188, H.192 Chain B: T.69, E.72, I.95, N.177, R.179 Chain D: S.97, N.99, E.100, S.102, R.104, Y.105 Ligands: 51Q.2, FAD.3 28 PLIP interactions: 16 interactions with chain A, 6 interactions with chain B, 6 interactions with chain D Hydrogen bonds: A:R.92, A:R.92, A:R.94, A:R.94, A:I.95, A:N.183, A:N.183, A:R.188, B:N.177, D:S.97, D:E.100, D:E.100 Water bridges: A:R.92, A:R.94, A:R.94, A:R.94, A:S.180, B:T.69, B:T.69, B:R.179, B:R.179, D:A.96, D:Y.98, D:S.102 Salt bridges: A:H.93, A:R.94, A:R.94, B:R.179 FAD.3: 21 residues within 4Å: Chain A: T.69, E.72, I.95, N.177, R.179 Chain B: R.92, H.93, R.94, I.95, N.183, L.187, R.188, H.192 Chain C: S.97, N.99, E.100, S.102, R.104, Y.105 Ligands: FAD.1, 51Q.4 26 PLIP interactions: 13 interactions with chain B, 6 interactions with chain C, 7 interactions with chain A Hydrogen bonds: B:R.92, B:R.92, B:R.94, B:R.94, B:I.95, B:N.183, B:N.183, C:S.97, C:E.100, C:E.100, A:T.69, A:N.177 Water bridges: B:R.92, B:R.94, B:S.180, C:A.96, C:Y.98, C:S.102, A:T.69, A:T.69, A:R.179, A:R.179 Salt bridges: B:H.93, B:R.94, B:R.94, A:R.179 FAD.5: 21 residues within 4Å: Chain B: S.97, N.99, E.100, S.102, R.104, Y.105 Chain C: R.92, H.93, R.94, I.95, N.183, L.187, R.188, H.192 Chain D: T.69, E.72, I.95, N.177, R.179 Ligands: 51Q.6, FAD.7 28 PLIP interactions: 6 interactions with chain B, 16 interactions with chain C, 6 interactions with chain D Hydrogen bonds: B:S.97, B:E.100, B:E.100, C:R.92, C:R.92, C:R.94, C:R.94, C:I.95, C:N.183, C:N.183, C:R.188, D:N.177 Water bridges: B:A.96, B:Y.98, B:S.102, C:R.92, C:R.94, C:R.94, C:R.94, C:S.180, D:T.69, D:T.69, D:R.179, D:R.179 Salt bridges: C:H.93, C:R.94, C:R.94, D:R.179 FAD.7: 21 residues within 4Å: Chain A: S.97, N.99, E.100, S.102, R.104, Y.105 Chain C: T.69, E.72, I.95, N.177, R.179 Chain D: R.92, H.93, R.94, I.95, N.183, L.187, R.188, H.192 Ligands: FAD.5, 51Q.8 26 PLIP interactions: 13 interactions with chain D, 6 interactions with chain A, 7 interactions with chain C Hydrogen bonds: D:R.92, D:R.92, D:R.94, D:R.94, D:I.95, D:N.183, D:N.183, A:S.97, A:E.100, A:E.100, C:T.69, C:N.177 Water bridges: D:R.92, D:R.94, D:S.180, A:A.96, A:Y.98, A:S.102, C:T.69, C:T.69, C:R.179, C:R.179 Salt bridges: D:H.93, D:R.94, D:R.94, C:R.179

4 x 51Q: (2S)-2-[(3-hydroxy-5-oxo-4,5-dihydro-1,2,4-triazin-6-yl)sulfanyl]propanoic acid(Non-covalent)

51Q.2: 10 residues within 4Å: Chain A: Q.89, R.92, R.188 Chain D: E.100, L.101, S.102, G.103, R.104, R.161 Ligands: FAD.1 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:S.102, D:G.103, D:R.104, D:R.104, A:Q.89, A:R.188, A:R.188 Salt bridges: D:R.161 Water bridges: A:Q.89 51Q.4: 10 residues within 4Å: Chain B: Q.89, R.92, R.188 Chain C: E.100, L.101, S.102, G.103, R.104, R.161 Ligands: FAD.3 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:S.102, C:G.103, C:R.104, C:R.104, B:Q.89, B:R.188, B:R.188 Salt bridges: C:R.161 Water bridges: B:Q.89 51Q.6: 10 residues within 4Å: Chain B: E.100, L.101, S.102, G.103, R.104, R.161 Chain C: Q.89, R.92, R.188 Ligands: FAD.5 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:S.102, B:G.103, B:R.104, B:R.104, C:Q.89, C:R.188, C:R.188 Salt bridges: B:R.161 Water bridges: C:Q.89 51Q.8: 10 residues within 4Å: Chain A: E.100, L.101, S.102, G.103, R.104, R.161 Chain D: Q.89, R.92, R.188 Ligands: FAD.7 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain A Hydrogen bonds: D:Q.89, D:R.188, D:R.188, A:S.102, A:G.103, A:R.104, A:R.104 Water bridges: D:Q.89 Salt bridges: A:R.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Surade, S., Identification of inhibitors targeting substrate-binding site in Mycobacterium tuberculosis FAD-dependent Thymidylate synthase (ThyX) through Virtual Screening: A New study de-fining the binding mechanism of Inhibitors. To Be Published

Release Date

2016-10-19

Peptides

Thymidylate synthase ThyX: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Thymidylate synthase ThyX