SMTL ID : 5epu.1

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with cytosine at 1.06A.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.06 Å

Oligo State

homo-hexamer

Ligands

6 x CYT: 6-AMINOPYRIMIDIN-2(1H)-ONE(Non-covalent)

CYT.1: 13 residues within 4Å: Chain A: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.219, I.220, R.222 Ligands: GOL.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.95, A:Q.165, A:Q.165, A:Q.165, A:R.167, A:R.167 CYT.10: 14 residues within 4Å: Chain B: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.219, I.220, R.222, P.228 Ligands: GOL.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.219 Hydrogen bonds: B:G.95, B:Q.165, B:Q.165, B:Q.165, B:R.167, B:R.167 Water bridges: B:M.196 CYT.13: 14 residues within 4Å: Chain C: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.219, I.220, R.222, P.228 Ligands: EDO.14 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.219 Hydrogen bonds: C:G.95, C:Q.165, C:Q.165, C:Q.165, C:R.167, C:R.167 Water bridges: C:M.196 CYT.17: 13 residues within 4Å: Chain D: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.219, I.220, R.222 Ligands: GOL.16 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.95, D:Q.165, D:Q.165, D:Q.165, D:R.167, D:R.167 Water bridges: D:T.94 CYT.21: 13 residues within 4Å: Chain E: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.219, I.220, R.222 Ligands: GOL.19 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:G.95, E:Q.165, E:Q.165, E:Q.165, E:R.167, E:R.167 CYT.27: 13 residues within 4Å: Chain F: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.219, I.220, R.222 Ligands: GOL.24 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:Q.165, F:Q.165, F:Q.165, F:R.167, F:R.167 Water bridges: F:T.93, F:M.196

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: F.161, Y.162, R.167, D.169, I.220 Chain B: F.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.167, A:R.167, A:D.169 Water bridges: A:D.169 GOL.3: 10 residues within 4Å: Chain A: I.68, R.90, T.93, F.161, E.195, M.196, E.197 Chain B: H.7, R.47 Ligands: CYT.1 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:T.93, A:M.196, A:E.197 Water bridges: A:R.90, B:R.47, B:R.47, B:R.47, B:R.47, B:R.47 GOL.7: 12 residues within 4Å: Chain A: F.6, H.7, R.47, I.75 Chain B: I.68, R.90, T.93, F.161, E.195, M.196, E.197 Ligands: CYT.10 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Water bridges: B:T.93, B:T.93, A:R.47, A:R.47, A:R.47 Hydrogen bonds: A:H.7 GOL.16: 13 residues within 4Å: Chain C: F.6, H.7, R.47, I.75 Chain D: I.68, G.69, R.90, T.93, F.161, E.195, M.196, E.197 Ligands: CYT.17 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:H.7, D:T.93, D:E.197 Water bridges: C:R.47, C:R.47, D:T.93, D:T.93 GOL.19: 11 residues within 4Å: Chain E: I.68, R.90, T.93, F.161, E.195, M.196, E.197 Chain F: H.7, R.47, I.75 Ligands: CYT.21 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:H.7, F:R.47, F:R.47 Water bridges: E:T.93, E:T.93 GOL.24: 11 residues within 4Å: Chain E: H.7, R.47, I.75 Chain F: I.68, T.93, T.94, F.161, E.195, M.196, E.197 Ligands: CYT.27 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:T.93, E:H.7 Water bridges: F:T.93, F:T.93, E:R.47

7 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.4: 1 residues within 4Å: Chain A: A.206 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain A: S.45 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain B: R.177 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Chain B: F.171 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain E: N.102, Q.224 No protein-ligand interaction detected (PLIP) MG.25: 3 residues within 4Å: Chain F: H.100, N.102 Ligands: MG.26 No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain F: N.102, Q.224 Ligands: MG.25 No protein-ligand interaction detected (PLIP)

3 x NA: SODIUM ION(Non-functional Binders)

NA.6: 8 residues within 4Å: Chain A: E.48, G.67, I.68, S.72 Chain B: E.48, G.67, I.68, S.72 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.48, B:I.68, B:S.72, A:I.68, A:I.68, A:S.72 Water bridges: B:S.72 NA.15: 8 residues within 4Å: Chain C: E.48, G.67, I.68, S.72 Chain D: E.48, G.67, I.68, S.72 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:I.68, C:S.72, D:E.48, D:I.68, D:S.72 Water bridges: C:S.72 NA.23: 8 residues within 4Å: Chain E: E.48, G.67, I.68, S.72 Chain F: E.48, G.67, I.68, S.72 8 PLIP interactions: 4 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:E.48, E:I.68, E:I.68, E:S.72, F:E.48, F:I.68, F:S.72 Water bridges: F:S.72

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 5 residues within 4Å: Chain B: V.103, I.220, N.221, Q.224, K.225 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain C: V.103, I.220, N.221, Q.224, K.225 Ligand excluded by PLIP

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

TRS.11: 9 residues within 4Å: Chain B: L.115, R.178, F.179, S.182, E.185, W.186 Chain C: P.124, E.126 Chain D: R.177 5 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: C:E.126, B:R.178, B:R.178, B:R.178 Water bridges: D:R.177 TRS.29: 9 residues within 4Å: Chain A: P.124, E.126 Chain B: R.177 Chain F: L.115, R.178, F.179, S.182, E.185, W.186 10 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B, 3 interactions with chain F Hydrogen bonds: A:E.126, F:R.178, F:R.178, F:R.178 Water bridges: A:E.126, A:E.126, B:R.177, B:R.177, B:R.177, B:R.177

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

EDO.14: 10 residues within 4Å: Chain C: I.68, T.93, F.161, M.196, E.197 Chain D: F.6, H.7, R.47, I.75 Ligands: CYT.13 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:T.93, D:H.7 Water bridges: C:T.93, C:T.93, C:T.93, D:R.47 EDO.22: 6 residues within 4Å: Chain E: E.166, R.167, Y.168, D.169, R.222, E.226 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Y.168, E:D.169 Water bridges: E:R.222, E:R.222, E:R.222 EDO.28: 6 residues within 4Å: Chain F: E.166, R.167, Y.168, D.169, R.222, E.226 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:Y.168, F:D.169 Water bridges: F:R.222, F:R.222, F:R.222

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 cytosine at 1.06A. To Be Published

Release Date

2016-11-23

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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