SMTL ID : 1pk7.1

Crystal Structure of E. coli purine nucleoside phosphorylase complexed with adenosine and sulfate/phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 6 residues within 4Å: Chain A: G.20, R.87, G.89, S.90 Chain D: R.43 Ligands: ADN.2 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain A Salt bridges: D:R.43, A:R.87 Hydrogen bonds: A:G.20, A:D.21, A:V.88, A:S.90, A:S.90 PO4.3: 6 residues within 4Å: Chain B: G.20, R.87, G.89, S.90 Chain F: R.43 Ligands: ADN.4 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:G.20, B:V.88, B:S.90, B:S.90 Water bridges: B:D.21, B:D.21 Salt bridges: B:R.87, F:R.43 PO4.5: 9 residues within 4Å: Chain C: P.19, G.20, R.24, R.87, V.88, G.89, S.90 Chain E: R.43 Ligands: ADN.6 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:G.20, C:S.90 Salt bridges: C:R.24, C:R.87, E:R.43 PO4.7: 6 residues within 4Å: Chain A: R.43 Chain D: G.20, R.87, G.89, S.90 Ligands: ADN.8 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:G.20, D:D.21, D:V.88, D:S.90, D:S.90 Salt bridges: D:R.87, A:R.43 PO4.9: 6 residues within 4Å: Chain C: R.43 Chain E: G.20, R.87, G.89, S.90 Ligands: ADN.10 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:G.20, E:V.88, E:S.90, E:S.90 Water bridges: E:D.21, E:D.21 Salt bridges: E:R.87, C:R.43 PO4.11: 9 residues within 4Å: Chain B: R.43 Chain F: P.19, G.20, R.24, R.87, V.88, G.89, S.90 Ligands: ADN.12 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain F Salt bridges: B:R.43, F:R.24, F:R.87 Hydrogen bonds: F:G.20, F:S.90

6 x ADN: ADENOSINE(Non-covalent)

ADN.2: 14 residues within 4Å: Chain A: M.64, R.87, S.90, C.91, G.92, F.159, E.179, M.180, E.181, S.203, D.204 Chain D: H.4, R.43 Ligands: PO4.1 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:R.87, A:M.180, A:E.181, A:S.203, A:D.204, D:H.4, D:R.43 ADN.4: 14 residues within 4Å: Chain B: R.87, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181, S.203, I.206 Chain F: H.4, R.43 Ligands: PO4.3 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:R.87, B:M.180, B:E.181, F:H.4 pi-Stacking: B:F.159 ADN.6: 15 residues within 4Å: Chain C: M.64, R.87, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181, S.203, D.204 Chain E: H.4, R.43 Ligands: PO4.5 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:R.87, C:M.180, C:E.181, C:D.204, E:H.4, E:R.43 ADN.8: 14 residues within 4Å: Chain A: H.4, R.43 Chain D: M.64, R.87, S.90, C.91, G.92, F.159, E.179, M.180, E.181, S.203, D.204 Ligands: PO4.7 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:R.87, D:M.180, D:E.181, D:S.203, D:D.204, A:H.4, A:R.43 ADN.10: 14 residues within 4Å: Chain C: H.4, R.43 Chain E: R.87, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181, S.203, I.206 Ligands: PO4.9 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:R.87, E:M.180, E:E.181, C:H.4 pi-Stacking: E:F.159 ADN.12: 15 residues within 4Å: Chain B: H.4, R.43 Chain F: M.64, R.87, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181, S.203, D.204 Ligands: PO4.11 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain F Hydrogen bonds: B:H.4, B:R.43, F:R.87, F:M.180, F:E.181, F:D.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bennett, E.M. et al., Structural basis for substrate specificity of Escherichia coli purine nucleoside phosphorylase. J.Biol.Chem. (2003)

Release Date

2003-11-25

Peptides

Purine nucleoside phosphorylase DeoD-type: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Purine nucleoside phosphorylase DeoD-type

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