SMTL ID : 4u2k.1

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with anticancer compound at 2.13 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-hexamer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: F.161, Q.165, E.195, M.196 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:H.7 Hydrogen bonds: A:Q.165, A:Q.165 EDO.2: 2 residues within 4Å: Chain A: R.178 Chain B: L.120 No protein-ligand interaction detected (PLIP) EDO.3: 3 residues within 4Å: Chain A: F.171, T.172 Chain B: S.208 No protein-ligand interaction detected (PLIP) EDO.5: 4 residues within 4Å: Chain C: I.68, F.161, M.196 Chain D: H.7 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Water bridges: C:E.197 Hydrogen bonds: D:H.7 EDO.6: 4 residues within 4Å: Chain C: G.95, F.161, R.167, I.220 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.167 Water bridges: C:Q.165 EDO.12: 8 residues within 4Å: Chain E: P.24, G.25, D.26, R.29, R.90, V.91, G.92 Chain F: R.47 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.25, E:D.26, E:R.29, F:R.47 EDO.13: 7 residues within 4Å: Chain E: R.90, V.91, G.92, T.94, E.195, V.215, A.216 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.90, E:V.215

2 x 4WR: 1-[(2R)-2,3-diaminopropyl]-5-fluoropyrimidine-2,4(1H,3H)-dione(Non-covalent)

4WR.4: 11 residues within 4Å: Chain A: H.7 Chain B: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.220 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.165, B:Q.165, B:R.167, B:R.167, A:H.7 Water bridges: B:E.197, B:E.197, B:E.197, A:R.47 4WR.10: 15 residues within 4Å: Chain C: H.7, R.47 Chain D: T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, E.197, I.219, I.220 Ligands: GOL.7, M5F.9 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.165, D:Q.165, D:R.167, D:R.167, D:E.197 Water bridges: D:M.196, C:R.47

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 10 residues within 4Å: Chain C: R.47 Chain D: P.24, G.25, D.26, G.67, R.90, V.91, E.197 Ligands: M5F.9, 4WR.10 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.25, D:D.26, D:G.67, D:R.90, C:R.47, C:R.47 Water bridges: D:T.93, D:T.93, D:E.197 GOL.11: 2 residues within 4Å: Chain E: K.250, K.253 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.253 Water bridges: E:D.134

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 7 residues within 4Å: Chain D: P.131, D.132, A.206, G.209, L.210, K.211, A.212 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.132, D:A.212 Water bridges: D:F.133, D:A.206, D:G.209

2 x M5F: 1-[(2S)-2,3-diaminopropyl]-5-fluoropyrimidine-2,4(1H,3H)-dione(Non-covalent)

M5F.9: 15 residues within 4Å: Chain C: F.6, H.7 Chain D: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.219, I.220 Ligands: GOL.7, 4WR.10 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Q.165, D:Q.165, D:R.167, D:R.167, C:H.7 Water bridges: D:M.196, D:E.197, C:R.47 M5F.15: 12 residues within 4Å: Chain E: F.6, H.7 Chain F: T.93, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.219, I.220 9 PLIP interactions: 2 interactions with chain E, 7 interactions with chain F Hydrogen bonds: E:H.7, F:Q.165, F:Q.165, F:R.167, F:R.167 Water bridges: E:H.7, F:M.196, F:E.197, F:E.197

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.14: 2 residues within 4Å: Chain F: F.6, R.47 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:F.6, F:R.47 Water bridges: F:H.7, F:R.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prokofev, I.I. et al., X-ray structure uridine phosphorylase from Vibrio cholerae in complex with new anticancer compound at 1.17 A resolution. To Be Published

Release Date

2015-07-29

Peptides

Uridine phosphorylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Uridine phosphorylase

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