SMTL ID : 1rxu.2 (2 other biounits)

E. coli uridine phosphorylase: thymidine phosphate complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 9 residues within 4Å: Chain A: G.26, D.27, R.30, R.91, I.92, G.93, T.94 Chain B: R.48 Ligands: THM.10 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.26, A:D.27, A:T.94 Salt bridges: A:R.30, A:R.91, B:R.48 PO4.2: 8 residues within 4Å: Chain A: R.48 Chain B: G.26, R.30, R.91, I.92, G.93, T.94 Ligands: THM.11 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.26, B:T.94 Salt bridges: B:R.30, B:R.91, A:R.48 PO4.3: 8 residues within 4Å: Chain C: G.26, R.30, R.91, I.92, G.93, T.94 Chain D: R.48 Ligands: THM.12 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 PO4.4: 8 residues within 4Å: Chain C: R.48 Chain D: G.26, R.30, R.91, I.92, G.93, T.94 Ligands: THM.13 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.26, D:T.94 Salt bridges: D:R.30, D:R.91, C:R.48 PO4.5: 9 residues within 4Å: Chain E: G.26, D.27, R.30, R.91, I.92, G.93, T.94 Chain F: R.48 Ligands: THM.14 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.26, E:T.94 Salt bridges: E:R.30, E:R.91, F:R.48 PO4.6: 8 residues within 4Å: Chain E: R.48 Chain F: G.26, R.30, R.91, I.92, G.93, T.94 Ligands: THM.15 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.26, F:T.94 Salt bridges: F:R.30, F:R.91, E:R.48

3 x K: POTASSIUM ION(Non-covalent)

K.7: 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 A, 2 interactions with chain B Metal complexes: A:E.49, A:I.69, A:S.73, B:I.69, B:S.73 K.8: 6 residues within 4Å: Chain C: E.49, I.69, S.73 Chain D: E.49, I.69, S.73 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Metal complexes: C:E.49, C:I.69, C:S.73, D:E.49, D:S.73 K.9: 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 F, 3 interactions with chain E Metal complexes: F:E.49, F:I.69, E:E.49, E:I.69, E:S.73

6 x THM: THYMIDINE(Non-covalent)

THM.10: 15 residues within 4Å: Chain A: I.69, T.94, T.95, G.96, F.162, Q.166, R.168, E.196, M.197, E.198, I.220, V.221, P.229 Chain B: H.8 Ligands: PO4.1 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.162, A:I.220, A:V.221, A:P.229 Hydrogen bonds: A:T.94, A:Q.166, A:Q.166, A:R.168, A:R.168, B:H.8 THM.11: 16 residues within 4Å: Chain A: H.8, R.48 Chain B: I.69, T.94, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, E.198, I.220, V.221, P.229 Ligands: PO4.2 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.220, B:V.221, B:P.229 Hydrogen bonds: B:T.94, B:Q.166, B:Q.166, B:R.168, B:R.168, A:H.8 pi-Stacking: B:F.162 THM.12: 15 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, I.220, V.221 Chain D: H.8 Ligands: PO4.3 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.162, C:M.197, C:I.220, C:V.221 Hydrogen bonds: C:Q.166, C:Q.166, C:R.168, C:R.168, D:H.8 THM.13: 17 residues within 4Å: Chain C: F.7, 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, P.229 Ligands: PO4.4 9 PLIP interactions: 1 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:H.8, D:Q.166, D:Q.166, D:R.168, D:R.168 Hydrophobic interactions: D:M.197, D:I.220, D:V.221, D:P.229 THM.14: 17 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, P.229 Chain F: H.8, R.48 Ligands: PO4.5 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:F.162, E:M.197, E:I.220, E:V.221, E:P.229 Hydrogen bonds: E:T.94, E:Q.166, E:Q.166, E:R.168, E:R.168, F:H.8 THM.15: 16 residues within 4Å: Chain E: H.8, R.48 Chain F: R.91, T.94, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, E.198, I.220, V.221, P.229 Ligands: PO4.6 12 PLIP interactions: 11 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:F.162, F:M.197, F:I.220, F:P.229 Hydrogen bonds: F:R.91, F:T.94, F:G.96, F:Q.166, F:Q.166, F:R.168, F:R.168, E:H.8

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
H

C
I

D
J

E
K

F
L

Uridine phosphorylase

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