SMTL ID : 1rxy.1

E. coli uridine phosphorylase: type-B native

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

3 x K: POTASSIUM ION(Non-covalent)

K.1: 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.7: 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.13: 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

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 6 residues within 4Å: Chain A: S.4, V.6, F.7, H.8, L.9, G.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.4, A:G.10 Salt bridges: A:H.47 ACT.8: 6 residues within 4Å: Chain C: S.4, V.6, F.7, H.8, L.9, G.10 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.4, C:G.10 Salt bridges: C:H.47 ACT.14: 6 residues within 4Å: Chain E: S.4, V.6, F.7, H.8, L.9, G.10 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.4, E:G.10 Salt bridges: E:H.47

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

SO4.3: 4 residues within 4Å: Chain A: R.48 Chain B: G.26, R.91, I.92 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.26 Water bridges: B:D.27, B:D.27, B:R.91, B:R.91, B:T.94, B:T.94, B:E.198, A:R.48 Salt bridges: B:R.91, A:R.48 SO4.9: 4 residues within 4Å: Chain C: R.48 Chain D: G.26, R.91, I.92 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.26 Water bridges: D:D.27, D:D.27, D:R.91, D:R.91, D:T.94, D:T.94, D:E.198, C:R.48 Salt bridges: D:R.91, C:R.48 SO4.15: 4 residues within 4Å: Chain E: R.48 Chain F: G.26, R.91, I.92 11 PLIP interactions: 9 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:G.26 Water bridges: F:D.27, F:D.27, F:R.91, F:R.91, F:T.94, F:T.94, F:E.198, E:R.48 Salt bridges: F:R.91, E:R.48

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: R.115, L.116, L.121, L.126, F.180 Chain D: E.127 No protein-ligand interaction detected (PLIP) GOL.5: 7 residues within 4Å: Chain B: R.115, L.116, L.121, L.126, H.179, F.180 Chain E: E.127 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E Water bridges: B:H.179, E:E.127 GOL.6: 12 residues within 4Å: Chain A: T.111, V.131, A.132, D.133, F.134, T.137 Chain D: T.111, V.131, A.132, D.133, F.134, T.137 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:A.132, A:T.111, A:T.137 GOL.10: 6 residues within 4Å: Chain C: R.115, L.116, L.121, L.126, F.180 Chain F: E.127 No protein-ligand interaction detected (PLIP) GOL.11: 7 residues within 4Å: Chain A: E.127 Chain D: R.115, L.116, L.121, L.126, H.179, F.180 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.127, A:E.127 GOL.12: 12 residues within 4Å: Chain C: T.111, V.131, A.132, D.133, F.134, T.137 Chain F: T.111, V.131, A.132, D.133, F.134, T.137 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:T.111, C:T.137, F:A.132 GOL.16: 6 residues within 4Å: Chain B: E.127 Chain E: R.115, L.116, L.121, L.126, F.180 No protein-ligand interaction detected (PLIP) GOL.17: 7 residues within 4Å: Chain C: E.127 Chain F: R.115, L.116, L.121, L.126, H.179, F.180 2 PLIP interactions: 2 interactions with chain C Water bridges: C:E.127, C:E.127 GOL.18: 12 residues within 4Å: Chain B: T.111, V.131, A.132, D.133, F.134, T.137 Chain E: T.111, V.131, A.132, D.133, F.134, T.137 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:T.111, E:T.137, B:A.132

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
A

B
B

C
A

D
B

E
A

F
B

Uridine phosphorylase

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