SMTL ID : 5lok.1

X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with cytidine and cytosine at 1.11 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.11 Å

Oligo State

homo-hexamer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: R.178 Chain B: L.120, P.124 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F Water bridges: B:A.123, F:E.126 EDO.9: 3 residues within 4Å: Chain A: L.120, P.124 Chain B: R.178 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:A.123, B:R.178 EDO.24: 3 residues within 4Å: Chain E: R.178 Chain F: L.120, P.124 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Water bridges: F:A.123, E:R.178

3 x K: POTASSIUM ION(Non-covalent)

K.2: 8 residues within 4Å: Chain A: E.48, G.67, I.68, S.72 Chain B: E.48, G.67, I.68, S.72 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Metal complexes: B:E.48, B:I.68, A:E.48, A:I.68, A:S.72 K.14: 8 residues within 4Å: Chain C: E.48, G.67, I.68, S.72 Chain D: E.48, G.67, I.68, S.72 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Metal complexes: C:E.48, C:I.68, C:S.72, D:E.48, D:I.68 K.25: 8 residues within 4Å: Chain E: E.48, G.67, I.68, S.72 Chain F: E.48, G.67, I.68, S.72 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain F Metal complexes: E:E.48, E:I.68, E:S.72, F:E.48, F:I.68

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

CTN.3: 23 residues within 4Å: Chain A: I.68, G.69, R.90, T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, E.197, I.219, I.220, R.222, P.228 Chain B: F.6, H.7, R.47, I.75 Ligands: CYT.4, GOL.5 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.90, A:T.93, A:Q.165, A:Q.165, A:R.167, A:R.167, A:M.196, A:E.197, B:H.7 Water bridges: A:T.93, A:T.93, A:T.93, B:R.47, B:R.47 CTN.10: 22 residues within 4Å: Chain A: F.6, H.7, R.47, I.75 Chain B: I.68, G.69, R.90, T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, E.197, I.219, I.220, R.222 Ligands: CYT.11, GOL.12 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.95, B:Q.165, B:Q.165, B:R.167, B:M.196, B:E.197, B:E.197, A:H.7 Water bridges: B:R.90, B:T.93, B:R.167, A:R.47, A:R.47, A:R.47 CTN.15: 21 residues within 4Å: Chain C: I.68, R.90, T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, E.197, I.219, I.220, R.222 Chain D: F.6, H.7, R.47, I.75 Ligands: CYT.16, GOL.17 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:R.90, C:Q.165, C:Q.165, C:R.167, C:M.196, C:E.197, D:H.7, D:R.47 Water bridges: C:T.93, C:T.93, C:R.167, D:R.47 CTN.19: 23 residues within 4Å: Chain C: F.6, H.7, R.47, I.75 Chain D: I.68, G.69, R.90, T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, E.197, I.219, I.220, R.222, P.228 Ligands: CYT.20, GOL.21 16 PLIP interactions: 10 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:R.90, D:T.93, D:Q.165, D:Q.165, D:R.167, D:R.167, D:M.196, D:E.197, D:E.197, C:H.7 Water bridges: D:T.93, C:R.47, C:R.47, C:R.47, C:R.47, C:R.47 CTN.26: 21 residues within 4Å: Chain E: I.68, R.90, T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, E.197, I.219, I.220, R.222 Chain F: F.6, H.7, R.47, I.75 Ligands: CYT.27, GOL.28 17 PLIP interactions: 12 interactions with chain E, 5 interactions with chain F Hydrogen bonds: E:R.90, E:Q.165, E:Q.165, E:R.167, E:E.195, E:E.195, E:M.196, E:E.197, F:H.7 Water bridges: E:T.93, E:T.93, E:R.167, E:E.197, F:R.47, F:R.47, F:R.47, F:R.47 CTN.30: 22 residues within 4Å: Chain E: F.6, H.7, R.47, I.75 Chain F: I.68, G.69, R.90, T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, E.197, I.219, I.220, R.222 Ligands: CYT.31, GOL.32 15 PLIP interactions: 10 interactions with chain F, 5 interactions with chain E Hydrogen bonds: F:Q.165, F:Q.165, F:R.167, F:M.196, F:E.197, F:E.197, E:H.7 Water bridges: F:R.90, F:T.93, F:R.167, F:E.195, E:R.47, E:R.47, E:R.47, E:R.47

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

CYT.4: 15 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, P.228 Ligands: CTN.3, GOL.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.219 Hydrogen bonds: A:G.95, A:Q.165, A:Q.165, A:Q.165, A:R.167, A:R.167 CYT.11: 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 Ligands: CTN.10, GOL.12 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.220 Hydrogen bonds: B:G.95, B:Q.165, B:Q.165, B:Q.165, B:R.167, B:R.167 CYT.16: 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 Ligands: CTN.15, GOL.17 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.95, C:Q.165, C:Q.165, C:Q.165, C:R.167, C:R.167 CYT.18: 2 residues within 4Å: Chain D: Y.168, G.173 2 PLIP interactions: 2 interactions with chain D Water bridges: D:Y.168 pi-Stacking: D:Y.168 CYT.20: 15 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, P.228 Ligands: CTN.19, GOL.21 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.219 Hydrogen bonds: D:G.95, D:Q.165, D:Q.165, D:Q.165, D:R.167, D:R.167 CYT.27: 14 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: CTN.26, GOL.28 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.31: 14 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: CTN.30, GOL.32 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:G.95, F:Q.165, F:Q.165, F:Q.165, F:R.167, F:R.167

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 12 residues within 4Å: Chain A: I.68, R.90, T.93, F.161, M.196, E.197 Chain B: F.6, H.7, R.47, I.75 Ligands: CTN.3, CYT.4 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.90, A:T.93, B:H.7 Water bridges: A:T.93, A:T.93, A:E.197, A:E.197, B:R.47, B:R.47 GOL.12: 11 residues within 4Å: Chain A: F.6, H.7, R.47 Chain B: I.68, G.69, T.93, F.161, M.196, E.197 Ligands: CTN.10, CYT.11 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.93, B:E.197, A:H.7 Water bridges: B:R.90, B:T.93, B:T.93, A:R.47, A:R.47 GOL.17: 11 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: CTN.15, CYT.16 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:H.7, D:R.47 Water bridges: D:R.47, D:R.47, C:T.93, C:T.93, C:T.93, C:E.197, C:E.197 GOL.21: 12 residues within 4Å: Chain C: F.6, H.7, R.47, I.75 Chain D: I.68, R.90, T.93, F.161, M.196, E.197 Ligands: CTN.19, CYT.20 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:R.90, D:T.93, C:R.47 Water bridges: D:T.93, D:E.197, C:R.47, C:R.47, C:R.47, C:R.47 GOL.28: 12 residues within 4Å: Chain E: I.68, R.90, T.93, F.161, M.196, E.197 Chain F: F.6, H.7, R.47, I.75 Ligands: CTN.26, CYT.27 7 PLIP interactions: 3 interactions with chain E, 4 interactions with chain F Water bridges: E:T.93, E:T.93, E:T.93, F:R.47, F:R.47, F:R.47 Hydrogen bonds: F:H.7 GOL.32: 12 residues within 4Å: Chain E: F.6, H.7, R.47 Chain F: I.68, G.69, R.90, T.93, F.161, M.196, E.197 Ligands: CTN.30, CYT.31 7 PLIP interactions: 2 interactions with chain F, 5 interactions with chain E Hydrogen bonds: F:E.197, E:H.7 Water bridges: F:R.90, E:R.47, E:R.47, E:R.47, E:R.47

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

SO4.6: 9 residues within 4Å: Chain A: P.24, G.25, D.26, R.29, V.91, G.92, T.93, E.237 Chain B: R.47 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.25, A:D.26, A:E.237, A:E.237 Water bridges: B:R.47 Salt bridges: B:R.47

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

CL.7: 6 residues within 4Å: Chain A: R.47 Chain B: P.24, G.25, D.26, R.29, G.92 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain B: V.103, I.220, N.221, Q.224, E.226, P.228 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain C: P.24, G.25, D.26, R.29, G.92 Chain D: R.47 Ligand excluded by PLIP CL.22: 6 residues within 4Å: Chain E: V.103, I.220, N.221, Q.224, E.226, P.228 Ligand excluded by PLIP CL.23: 6 residues within 4Å: Chain E: P.24, G.25, D.26, R.29, G.92 Chain F: R.47 Ligand excluded by PLIP CL.29: 6 residues within 4Å: Chain E: R.47 Chain F: P.24, G.25, D.26, R.29, G.92 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prokofev, I.I. et al., X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with cytidine and cytosine at 1.11 A resolution. To Be Published

Release Date

2017-08-23

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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