SMTL ID : 1rxs.3 (4 other biounits)

E. coli uridine phosphorylase: 2'-deoxyuridine phosphate complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-hexamer

Ligands

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 8 residues within 4Å: Chain A: G.26, R.30, R.91, I.92, G.93, T.94 Chain B: R.48 Ligands: DUR.3 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.26, A:T.94, A:E.198 Salt bridges: A:R.30, A:R.91, B:R.48 PO4.4: 9 residues within 4Å: Chain A: R.48 Chain B: G.26, R.30, R.91, I.92, G.93, T.94, E.198 Ligands: DUR.5 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.26, B:T.94, B:E.198 Salt bridges: B:R.30, B:R.91, A:R.48 PO4.6: 8 residues within 4Å: Chain C: G.26, R.30, R.91, I.92, G.93, T.94 Chain D: R.48 Ligands: DUR.7 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.26, C:T.94 Salt bridges: C:R.30, C:R.91, D:R.48 PO4.9: 8 residues within 4Å: Chain C: R.48 Chain D: G.26, R.30, R.91, I.92, G.93, T.94 Ligands: DUR.11 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.26, D:D.27, D:T.94, D:E.198 Salt bridges: D:R.30, D:R.91, C:R.48 PO4.13: 8 residues within 4Å: Chain E: G.26, R.30, R.91, I.92, G.93, T.94 Chain F: R.48 Ligands: DUR.14 5 PLIP interactions: 1 interactions with chain F, 4 interactions with chain E Salt bridges: F:R.48, E:R.30, E:R.91 Hydrogen bonds: E:G.26, E:T.94 PO4.16: 9 residues within 4Å: Chain E: R.48 Chain F: G.26, R.30, R.91, I.92, G.93, T.94, E.198 Ligands: DUR.18 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.26, F:T.94, F:E.198 Salt bridges: F:R.30, F:R.91, E:R.48

3 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: E.49, I.69, S.73 Chain B: E.49, I.69, S.73 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.49, B:I.69, B:S.73, A:E.49, A:I.69 K.10: 6 residues within 4Å: Chain C: E.49, I.69, S.73 Chain D: E.49, I.69, S.73 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Metal complexes: C:E.49, C:I.69, D:E.49, D:I.69, D:S.73 K.17: 6 residues within 4Å: Chain E: E.49, I.69, S.73 Chain F: E.49, I.69, S.73 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain F Metal complexes: E:E.49, E:I.69, F:E.49, F:I.69, F:S.73

6 x DUR: 2'-DEOXYURIDINE(Non-covalent)

DUR.3: 16 residues within 4Å: Chain A: I.69, R.91, T.94, T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, E.198, I.220, V.221 Chain B: H.8 Ligands: PO4.1 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.220 Hydrogen bonds: A:G.96, A:Q.166, A:Q.166, A:R.168, A:R.168, A:E.198, B:H.8 DUR.5: 15 residues within 4Å: Chain A: H.8 Chain B: I.69, T.94, T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, E.198, I.220, V.221 Ligands: PO4.4 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.220 Hydrogen bonds: B:G.96, B:Q.166, B:Q.166, B:R.168, B:R.168, B:E.198, A:H.8 DUR.7: 13 residues within 4Å: Chain C: I.69, T.94, T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, E.198 Chain D: H.8 Ligands: PO4.6 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:M.197 Hydrogen bonds: C:Q.166, C:Q.166, C:R.168, C:R.168, C:E.198, D:H.8 DUR.11: 15 residues within 4Å: Chain C: H.8 Chain D: I.69, T.94, T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, E.198, I.220, V.221 Ligands: PO4.9 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:E.196, D:M.197, D:I.220 Hydrogen bonds: D:T.94, D:Q.166, D:Q.166, D:R.168, D:R.168, D:E.198, C:H.8 DUR.14: 15 residues within 4Å: Chain E: I.69, T.94, T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, E.198, I.220, V.221 Chain F: H.8 Ligands: PO4.13 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:I.220 Hydrogen bonds: E:G.96, E:Q.166, E:Q.166, E:R.168, E:R.168, E:E.198, F:H.8 DUR.18: 15 residues within 4Å: Chain E: H.8 Chain F: I.69, T.94, T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, E.198, I.220, V.221 Ligands: PO4.16 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:E.196, F:I.220 Hydrogen bonds: F:R.91, F:Q.166, F:Q.166, F:R.168, F:R.168, F:E.198, E:H.8

4 x V7O: META VANADATE(Non-covalent)

V7O.8: 5 residues within 4Å: Chain A: R.178, H.179 Chain C: H.179 Chain E: H.179 Ligands: V7O.15 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:H.179, A:H.179 V7O.12: 7 residues within 4Å: Chain B: R.178, H.179 Chain D: R.178, H.179 Chain F: R.178, H.179 Ligands: V7O.19 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain F, 1 interactions with chain D Hydrogen bonds: B:R.178, B:H.179, F:H.179, D:R.178 V7O.15: 7 residues within 4Å: Chain A: R.178, H.179 Chain C: R.178, H.179 Chain E: R.178, H.179 Ligands: V7O.8 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 interactions with chain E Hydrogen bonds: A:R.178, A:H.179, C:H.179, E:H.179 V7O.19: 4 residues within 4Å: Chain B: H.179 Chain D: H.179 Chain F: H.179 Ligands: V7O.12 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:H.179, F:H.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caradoc-Davies, T.T. et al., Crystal structures of escherichia coli uridine phosphorylase in two native and three complexed forms reveal basis of substrate specificity, induced conformational changes and influence of potassium. J.Mol.Biol. (2004)

Release Date

2004-04-13

Peptides

Uridine phosphorylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
P

C
H

D
h

E
I

F
i

Uridine phosphorylase

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