SMTL ID : 4eaf.1

Thymidine phosphorylase from E.coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: K.84, H.85, S.86, S.95, S.113, T.123 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.86, A:S.95, A:S.113, A:S.113, A:T.123 Water bridges: A:K.84, A:H.85, A:H.85, A:G.114, A:T.123 Salt bridges: A:K.84, A:H.85 SO4.2: 7 residues within 4Å: Chain A: A.175, T.176, V.177, D.178 Chain B: Q.5, R.9, R.12 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:A.175, A:V.177, A:D.178 Water bridges: B:R.9, B:R.12, B:R.12 Salt bridges: B:R.9, B:R.12 SO4.3: 3 residues within 4Å: Chain A: R.257, T.340, H.403 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.257, A:R.257, A:T.340, A:T.340 Salt bridges: A:R.257, A:H.403 SO4.4: 2 residues within 4Å: Chain A: H.15, A.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.16 Salt bridges: A:H.15 SO4.5: 2 residues within 4Å: Chain A: R.234, K.288 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.288, A:K.288 Salt bridges: A:R.234, A:K.288 SO4.6: 2 residues within 4Å: Chain A: Q.372, A.373 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.373 Water bridges: A:S.374, A:S.374 SO4.7: 2 residues within 4Å: Chain A: R.437, S.439 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.439, A:S.439 Water bridges: A:R.437, A:E.440 Salt bridges: A:R.437 SO4.10: 6 residues within 4Å: Chain B: K.84, H.85, S.86, S.95, S.113, T.123 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.86, B:S.95, B:S.113, B:S.113, B:T.123 Water bridges: B:K.84, B:G.114, B:T.123 Salt bridges: B:K.84, B:H.85 SO4.11: 7 residues within 4Å: Chain A: Q.5, R.9, R.12 Chain B: A.175, T.176, V.177, D.178 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:A.175, B:V.177, B:D.178 Water bridges: B:D.178, A:R.9, A:R.12 Salt bridges: A:R.9, A:R.12 SO4.12: 3 residues within 4Å: Chain B: R.257, T.340, H.403 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.340 Water bridges: B:R.257, B:R.257, B:T.340 Salt bridges: B:R.257, B:H.403 SO4.13: 2 residues within 4Å: Chain B: H.15, A.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.16 Salt bridges: B:H.15 SO4.14: 2 residues within 4Å: Chain B: R.234, K.288 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.288, B:K.288 Salt bridges: B:R.234, B:K.288 SO4.15: 2 residues within 4Å: Chain B: Q.372, A.373 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.373 Water bridges: B:S.374, B:S.374 SO4.16: 2 residues within 4Å: Chain B: R.437, S.439 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.439, B:S.439 Water bridges: B:R.437 Salt bridges: B:R.437

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain A: R.268, P.270, F.273 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.268 Water bridges: A:P.270 GOL.9: 5 residues within 4Å: Chain A: F.2, L.3, A.4, Q.5, Q.38 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.4, A:Q.5, A:Q.38 GOL.17: 3 residues within 4Å: Chain B: R.268, P.270, F.273 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.268 Water bridges: B:P.270 GOL.18: 5 residues within 4Å: Chain B: F.2, L.3, A.4, Q.5, Q.38 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.4, B:Q.5, B:Q.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Timofeev, V.I. et al., Thymidine phosphorylase from E.coli. To be Published

Release Date

2013-03-27

Peptides

Thymidine phosphorylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Thymidine phosphorylase

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