SMTL ID : 4ead.1

Thymidine phosphorylase from E.coli with 3'-azido-2'-fluoro-dideoxyuridine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x 0NP: 2',3'-dideoxy-2'-fluoro-3'-triaza-1,2-dien-2-ium-1-yluridine(Non-covalent)

0NP.1: 13 residues within 4Å: Chain A: T.87, L.117, D.164, Y.168, R.171, V.177, I.183, S.186, I.187, K.190, F.210, M.211, L.220 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.117 Hydrogen bonds: A:R.171, A:R.171, A:S.186, A:S.186, A:K.190 Water bridges: A:T.87, A:L.117, A:K.204 pi-Stacking: A:Y.168 0NP.12: 13 residues within 4Å: Chain B: T.87, L.117, D.164, Y.168, R.171, V.177, I.183, S.186, I.187, K.190, F.210, M.211, L.220 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.117 Hydrogen bonds: B:R.171, B:R.171, B:S.186, B:S.186, B:K.190 Water bridges: B:T.87, B:L.117, B:K.204 pi-Stacking: B:Y.168

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

SO4.2: 6 residues within 4Å: Chain A: K.84, H.85, S.86, S.95, S.113, T.123 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.86, A:S.95, A:S.113, A:T.123, A:T.123 Water bridges: A:K.84, A:H.85, A:H.85, A:T.123 Salt bridges: A:K.84, A:H.85 SO4.3: 8 residues within 4Å: Chain A: Q.5, R.9, R.12 Chain B: A.175, T.176, V.177, D.178, F.210 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Water bridges: A:Q.5, A:R.12, B:D.178 Salt bridges: A:R.9, A:R.12 Hydrogen bonds: B:V.177, B:D.178 SO4.4: 2 residues within 4Å: Chain A: H.15, A.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.16 Water bridges: A:H.15 Salt bridges: A:H.15 SO4.6: 2 residues within 4Å: Chain A: R.234, K.288 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.234, A:K.288 SO4.10: 4 residues within 4Å: Chain A: R.257, T.336, T.340, H.403 4 PLIP interactions: 4 interactions with chain A Water bridges: A:T.340, A:T.340 Salt bridges: A:R.257, A:H.403 SO4.11: 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 SO4.13: 6 residues within 4Å: Chain B: K.84, H.85, S.86, S.95, S.113, T.123 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.86, B:S.95, B:S.113, B:T.123, B:T.123 Water bridges: B:K.84, B:T.123 Salt bridges: B:K.84, B:H.85 SO4.14: 8 residues within 4Å: Chain A: A.175, T.176, V.177, D.178, F.210 Chain B: Q.5, R.9, R.12 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:V.177, A:D.178 Water bridges: B:Q.5, B:R.12, B:R.12 Salt bridges: B:R.9, B:R.12 SO4.15: 2 residues within 4Å: Chain B: H.15, A.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.16 Water bridges: B:H.15 Salt bridges: B:H.15 SO4.17: 2 residues within 4Å: Chain B: R.234, K.288 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.234, B:K.288 SO4.21: 4 residues within 4Å: Chain B: R.257, T.336, T.340, H.403 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.340 Water bridges: B:T.340 Salt bridges: B:R.257, B:H.403 SO4.22: 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

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: F.2, L.3, A.4, Q.5, Q.38 Ligands: GOL.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.2, A:A.4, A:Q.5, A:Q.38 GOL.7: 7 residues within 4Å: Chain A: G.116, L.117, G.118, R.370, R.371, Q.372, A.373 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.116, A:G.118, A:Q.372 Water bridges: A:R.370 GOL.8: 2 residues within 4Å: Chain A: Q.372, A.373 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.373 GOL.9: 5 residues within 4Å: Chain A: L.3, Q.5, E.6, R.9 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.9, A:R.9 Water bridges: A:Q.5 GOL.16: 6 residues within 4Å: Chain B: F.2, L.3, A.4, Q.5, Q.38 Ligands: GOL.20 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.2, B:A.4, B:Q.5, B:Q.38 GOL.18: 7 residues within 4Å: Chain B: G.116, L.117, G.118, R.370, R.371, Q.372, A.373 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.116, B:G.118, B:Q.372 Water bridges: B:R.370 GOL.19: 2 residues within 4Å: Chain B: Q.372, A.373 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.373 GOL.20: 5 residues within 4Å: Chain B: L.3, Q.5, E.6, R.9 Ligands: GOL.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.9, B:R.9 Water bridges: B:Q.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Timofeev, V.I. et al., Thymidine phosphorylase from E.coli with 3'-azido-2'-fluoro-dideoxyuridine. 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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