SMTL ID : 6z9z.1

Atomic resolution X-ray structure of the Uridine phosphorylase from Vibrio cholerae on crystals grown under microgravity

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.04 Å

Oligo State

homo-hexamer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: I.68, G.69, R.90, F.161, E.195, M.196, E.197 Chain B: H.7, R.47 Ligands: EDO.2 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Water bridges: B:R.47, B:R.47, A:R.90 Hydrogen bonds: A:E.195, A:M.196, A:E.197, A:E.197 GOL.6: 9 residues within 4Å: Chain A: H.7, R.47 Chain B: I.68, G.69, R.90, F.161, E.195, M.196, E.197 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.195, B:M.196, B:E.197, B:E.197 Water bridges: B:R.90, B:R.90, B:E.197, A:H.7, A:R.47, A:R.47 GOL.13: 6 residues within 4Å: Chain C: F.161, Y.162, R.167, D.169, I.220 Chain D: F.6 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.167, C:D.169 Water bridges: C:R.167, C:R.167 GOL.18: 11 residues within 4Å: Chain C: F.6, H.7, R.47, I.75 Chain D: I.68, G.69, R.90, F.161, Q.165, M.196, E.197 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:E.197, C:R.47 Water bridges: C:R.47 GOL.25: 12 residues within 4Å: Chain E: I.68, G.69, R.90, F.161, Q.165, E.195, M.196, E.197 Chain F: F.6, H.7, R.47, I.75 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Water bridges: F:R.47 Hydrogen bonds: E:E.197

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

EDO.2: 10 residues within 4Å: Chain A: T.94, G.95, F.161, Q.165, R.167, F.194, E.195, I.220, R.222 Ligands: GOL.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.94, A:G.95, A:R.167, A:F.194 Water bridges: A:R.167 EDO.3: 4 residues within 4Å: Chain A: R.178 Chain B: L.120, P.124, M.125 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B, 1 interactions with chain A Water bridges: F:E.126, B:A.123, A:R.178 EDO.7: 6 residues within 4Å: Chain B: E.166, R.167, Y.168, D.169, R.222, E.226 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.166, B:Y.168, B:D.169 Water bridges: B:R.167, B:D.169, B:R.222, B:R.222 EDO.8: 4 residues within 4Å: Chain A: Q.82 Chain B: D.169, T.170, F.171 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.169 Water bridges: A:Q.82, A:Q.82 EDO.9: 4 residues within 4Å: Chain A: L.120, P.124, M.125 Chain B: R.178 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Water bridges: B:R.178, C:E.126, A:A.123 EDO.11: 9 residues within 4Å: Chain C: I.68, G.69, R.90, F.161, M.196, E.197 Chain D: H.7, R.47, I.75 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.197 Water bridges: D:R.47 EDO.12: 6 residues within 4Å: Chain B: E.126 Chain C: R.178 Chain D: L.120, P.124, M.125 Ligands: PEG.23 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Water bridges: C:R.178, D:A.123 EDO.19: 9 residues within 4Å: Chain D: L.36, M.37, D.38, E.55, L.56, D.57, G.58, V.245, R.249 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.55, D:D.57, D:D.57, D:R.249, D:R.249 Water bridges: D:G.58 EDO.24: 5 residues within 4Å: Chain D: E.126 Chain E: R.178 Chain F: L.120, P.124, M.125 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Water bridges: E:R.178, F:A.123 EDO.26: 5 residues within 4Å: Chain E: A.28, Q.31, F.42, T.50, Y.52 No protein-ligand interaction detected (PLIP) EDO.31: 8 residues within 4Å: Chain E: R.47, I.75 Chain F: I.68, G.69, R.90, F.161, M.196, E.197 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Water bridges: E:R.47 Hydrogen bonds: F:E.197 EDO.32: 4 residues within 4Å: Chain E: L.120, P.124, M.125 Chain F: R.178 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Water bridges: F:R.178, E:A.123

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

NA.4: 1 residues within 4Å: Chain A: Q.180 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.180 NA.5: 8 residues within 4Å: Chain A: E.48, G.67, I.68, S.72 Chain B: E.48, G.67, I.68, S.72 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:I.68, A:I.68, B:I.68 Water bridges: B:S.72 NA.10: 2 residues within 4Å: Chain B: N.102, Q.224 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.102 Water bridges: B:N.102 NA.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 D, 2 interactions with chain C Hydrogen bonds: D:I.68, D:I.68, C:E.48, C:I.68 Water bridges: D:S.72 NA.15: 1 residues within 4Å: Chain C: Q.180 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.180 Water bridges: C:Q.180 NA.16: 1 residues within 4Å: Chain C: A.206 No protein-ligand interaction detected (PLIP) NA.20: 10 residues within 4Å: Chain D: R.114, M.125, E.126, F.127, P.128 Chain E: R.114, M.125, E.126, F.127, P.128 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:M.125 NA.21: 2 residues within 4Å: Chain D: R.177, Q.180 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.180, D:Q.180 NA.27: 1 residues within 4Å: Chain E: A.206 No protein-ligand interaction detected (PLIP) NA.28: 2 residues within 4Å: Chain E: R.177, Q.180 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.180, E:Q.180 NA.30: 8 residues within 4Å: Chain E: E.48, G.67, I.68, S.72 Chain F: E.48, G.67, I.68, S.72 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:E.48, E:I.68, F:E.48, F:I.68, F:I.68 Water bridges: E:S.72

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

PEG.17: 1 residues within 4Å: Chain C: D.38 3 PLIP interactions: 3 interactions with chain C Water bridges: C:D.38, C:D.38, C:D.57 PEG.23: 5 residues within 4Å: Chain C: L.120, P.124, M.125 Chain D: R.178 Ligands: EDO.12 1 PLIP interactions: 1 interactions with chain D Water bridges: D:R.178

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

MG.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.29: 1 residues within 4Å: Chain E: F.171 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eistrikh-Heller, P.A. et al., Crystallization in Microgravity and the Atomic-Resolution Structure of Uridine Phosphorylase from Vibrio cholerae. Crystallography Reports (2021)

Release Date

2021-06-30

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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