SMTL ID : 4r2x.1

Unique conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of Shewanella oneidensis uridine phosphorylase in the free form and in complex with uridine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.93 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 11 residues within 4Å: Chain A: G.24, D.25, R.28, I.67, R.89, V.90, G.91, T.92, E.196 Chain B: R.46 Ligands: GOL.3 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.24, A:T.92, A:T.92, A:E.196 Salt bridges: A:R.28, A:R.89, B:R.46 SO4.7: 11 residues within 4Å: Chain A: R.46 Chain B: G.24, D.25, R.28, I.67, R.89, V.90, G.91, T.92, E.196 Ligands: GOL.9 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.24, B:T.92, B:T.92 Salt bridges: B:R.28, B:R.89, A:R.46 SO4.12: 3 residues within 4Å: Chain A: R.176 Chain C: R.176 Chain E: R.176 5 PLIP interactions: 1 interactions with chain E, 2 interactions with chain C, 2 interactions with chain A Salt bridges: E:R.176, C:R.176, A:R.176 Water bridges: C:R.176, A:R.176 SO4.14: 11 residues within 4Å: Chain C: P.23, G.24, D.25, R.28, I.67, R.89, V.90, G.91, T.92 Chain D: R.46 Ligands: GOL.13 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:G.24, C:T.92 Water bridges: C:R.28, C:R.28, C:E.196, D:R.46, D:R.46 Salt bridges: C:R.28, C:R.89, D:R.46 SO4.17: 11 residues within 4Å: Chain C: R.46 Chain D: G.24, D.25, R.28, I.67, R.89, V.90, G.91, T.92, E.196 Ligands: GOL.21 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.24, D:V.90, D:T.92 Salt bridges: D:R.28, D:R.89, C:R.46 SO4.22: 11 residues within 4Å: Chain E: P.23, G.24, R.28, I.67, R.89, V.90, G.91, T.92, E.196 Chain F: R.46 Ligands: GOL.24 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.24, E:T.92, E:E.196 Salt bridges: E:R.28, E:R.89, F:R.46 SO4.27: 3 residues within 4Å: Chain B: R.176 Chain D: R.176 Chain F: R.176 5 PLIP interactions: 1 interactions with chain F, 2 interactions with chain D, 2 interactions with chain B Salt bridges: F:R.176, D:R.176, B:R.176 Water bridges: D:R.176, B:R.176 SO4.30: 11 residues within 4Å: Chain E: R.46 Chain F: P.23, G.24, D.25, R.28, I.67, R.89, V.90, G.91, T.92 Ligands: GOL.29 6 PLIP interactions: 1 interactions with chain E, 5 interactions with chain F Salt bridges: E:R.46, F:R.28, F:R.89 Hydrogen bonds: F:G.24, F:T.92, F:T.92

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

CL.2: 5 residues within 4Å: Chain A: G.94, F.160, Q.164, R.166, V.219 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: G.94, F.160, Q.164, R.166, V.219 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain D: G.94, F.160, Q.164, R.166, V.219 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain E: G.94, F.160, Q.164, R.166, V.219 Ligand excluded by PLIP

19 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 12 residues within 4Å: Chain A: G.24, I.67, R.89, T.92, T.93, F.160, Y.193, E.194, M.195, E.196 Chain B: R.46 Ligands: SO4.1 Ligand excluded by PLIP GOL.4: 11 residues within 4Å: Chain A: V.129, A.130, N.131, F.132, A.205, R.210 Chain D: Q.109, I.151, G.152, V.153, G.189 Ligand excluded by PLIP GOL.5: 9 residues within 4Å: Chain A: L.114, R.177, F.178, S.181, E.184, W.185 Chain C: R.176 Chain D: P.123, E.125 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: A.141, D.144, A.145, I.242, A.245, K.249 Ligand excluded by PLIP GOL.9: 14 residues within 4Å: Chain A: H.6, R.46, I.74 Chain B: I.67, G.68, R.89, T.92, T.93, F.160, Y.193, E.194, M.195, E.196 Ligands: SO4.7 Ligand excluded by PLIP GOL.10: 9 residues within 4Å: Chain B: L.114, R.177, F.178, S.181, E.184, W.185 Chain E: P.123, E.125 Chain F: R.176 Ligand excluded by PLIP GOL.11: 11 residues within 4Å: Chain B: V.129, A.130, N.131, F.132, A.205, W.209, R.210 Chain E: Q.109, I.151, G.152, V.153 Ligand excluded by PLIP GOL.13: 11 residues within 4Å: Chain C: I.67, R.89, T.92, F.160, Q.164, E.194, M.195, E.196 Chain D: H.6, R.46 Ligands: SO4.14 Ligand excluded by PLIP GOL.15: 11 residues within 4Å: Chain C: V.129, A.130, N.131, F.132, A.205, W.209, R.210 Chain F: Q.109, I.151, G.152, V.153 Ligand excluded by PLIP GOL.16: 9 residues within 4Å: Chain C: L.114, R.177, F.178, S.181, E.184, W.185 Chain E: R.176 Chain F: P.123, E.125 Ligand excluded by PLIP GOL.19: 9 residues within 4Å: Chain A: P.123, E.125 Chain B: R.176 Chain D: L.114, R.177, F.178, S.181, E.184, W.185 Ligand excluded by PLIP GOL.20: 11 residues within 4Å: Chain A: Q.109, I.151, G.152, V.153, G.189 Chain D: V.129, A.130, N.131, F.132, A.205, R.210 Ligand excluded by PLIP GOL.21: 13 residues within 4Å: Chain C: H.6, R.46 Chain D: I.67, R.89, T.92, T.93, F.160, Q.164, Y.193, E.194, M.195, E.196 Ligands: SO4.17 Ligand excluded by PLIP GOL.24: 11 residues within 4Å: Chain E: I.67, R.89, T.92, T.93, Q.164, Y.193, E.194, M.195, E.196 Chain F: R.46 Ligands: SO4.22 Ligand excluded by PLIP GOL.25: 11 residues within 4Å: Chain B: Q.109, I.151, G.152, V.153, G.189 Chain E: V.129, A.130, N.131, F.132, A.205, R.210 Ligand excluded by PLIP GOL.26: 9 residues within 4Å: Chain A: R.176 Chain B: P.123, E.125 Chain E: L.114, R.177, F.178, S.181, E.184, W.185 Ligand excluded by PLIP GOL.28: 11 residues within 4Å: Chain C: Q.109, I.151, G.152, V.153 Chain F: V.129, A.130, N.131, F.132, A.205, W.209, R.210 Ligand excluded by PLIP GOL.29: 11 residues within 4Å: Chain E: H.6, R.46 Chain F: I.67, R.89, T.92, F.160, Q.164, E.194, M.195, E.196 Ligands: SO4.30 Ligand excluded by PLIP GOL.31: 9 residues within 4Å: Chain C: P.123, E.125 Chain D: R.176 Chain F: L.114, R.177, F.178, S.181, E.184, W.185 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Safonova, T.N. et al., High-syn conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of Shewanella oneidensis MR-1 uridine phosphorylase in the free form and in complex with uridine. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-12-10

Peptides

uridine phosphorylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
F

E
A

F
B

uridine phosphorylase

Related Entries With Identical Sequence