SMTL ID : 5ey3.1

X-ray structure of the thymidine phosphorylase from Salmonella typhimurium in complex with cytidine and sulphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: Q.7, R.11, R.14 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.14, A:R.14 Salt bridges: A:R.11, A:R.14 SO4.2: 2 residues within 4Å: Chain A: H.17, A.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.18 Salt bridges: A:H.17 SO4.3: 4 residues within 4Å: Chain A: A.177, T.178, V.179, D.180 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.179, A:D.180 Water bridges: A:D.180 SO4.4: 5 residues within 4Å: Chain A: S.115, G.116, G.123, G.124, T.125 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.115, A:S.115, A:G.116, A:T.125 Water bridges: A:S.97 SO4.5: 2 residues within 4Å: Chain A: R.143, K.323 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.143, A:K.323 SO4.8: 6 residues within 4Å: Chain B: K.86, H.87, S.88, S.97, S.115, T.125 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.88, B:S.97, B:S.115, B:T.125, B:T.125 Water bridges: B:K.86, B:K.86, B:H.87, B:G.116, B:G.116 Salt bridges: B:K.86, B:H.87 SO4.9: 3 residues within 4Å: Chain B: Y.269, P.272, R.390 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.390 SO4.10: 3 residues within 4Å: Chain B: P.272, R.273, R.390 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.390 SO4.11: 2 residues within 4Å: Chain B: R.25, N.29 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.29 Salt bridges: B:R.25

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: R.270, F.275, Q.303 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.270, A:R.270, A:Q.303, A:Q.303 GOL.12: 4 residues within 4Å: Chain B: R.270, P.272, F.275, Q.303 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.270, B:R.270, B:Q.303

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 3 residues within 4Å: Chain A: P.82, G.289, Q.290 No protein-ligand interaction detected (PLIP)

1 x CTN: 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE(Non-covalent)

CTN.13: 12 residues within 4Å: Chain A: R.117, E.130, F.138, R.372, A.375, D.377 Chain B: D.52, R.58, I.182, A.221, E.224, A.225 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.58, B:R.58, A:R.117, A:R.117, A:D.377

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Balaev, V.V. et al., X-ray structure of the thymidine phosphorylase from Salmonella typhimurium in complex with cytidine and sulphate. To Be Published

Release Date

2016-12-07

Peptides

Thymidine phosphorylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidine phosphorylase