SMTL ID : 1pke.1

Crystal Structure of E. coli purine nucleoside phosphorylase complexed with 2-fluoro-2'-deoxyadenosine and sulfate/phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

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

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

6 x 2FD: 5-(6-AMINO-2-FLUORO-PURIN-9-YL)-2-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-OL(Non-covalent)

2FD.2: 14 residues within 4Å: Chain A: M.64, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181, S.203, D.204 Chain D: H.4, R.43 Ligands: PO4.1 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:E.179 Hydrogen bonds: A:D.204, D:H.4, D:R.43 Water bridges: A:S.203 2FD.4: 14 residues within 4Å: Chain B: M.64, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181, S.203, D.204 Chain F: H.4, R.43 Ligands: PO4.3 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain F Hydrophobic interactions: B:E.179 Hydrogen bonds: B:D.204, F:H.4, F:R.43 2FD.6: 15 residues within 4Å: Chain C: M.64, S.90, C.91, G.92, A.156, F.159, V.178, E.179, M.180, E.181, S.203, D.204 Chain E: H.4, R.43 Ligands: PO4.5 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: C:E.179 Hydrogen bonds: C:D.204, E:H.4, E:R.43 Water bridges: C:S.90 2FD.8: 14 residues within 4Å: Chain A: H.4, R.43 Chain D: M.64, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181, S.203, D.204 Ligands: PO4.7 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:E.179 Hydrogen bonds: D:D.204, A:H.4, A:R.43 Water bridges: D:S.203 2FD.10: 14 residues within 4Å: Chain C: H.4, R.43 Chain E: M.64, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181, S.203, D.204 Ligands: PO4.9 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:E.179 Hydrogen bonds: E:D.204, C:H.4, C:R.43 2FD.12: 15 residues within 4Å: Chain B: H.4, R.43 Chain F: M.64, S.90, C.91, G.92, A.156, F.159, V.178, E.179, M.180, E.181, S.203, D.204 Ligands: PO4.11 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain B Hydrophobic interactions: F:E.179 Hydrogen bonds: F:D.204, B:H.4, B:R.43 Water bridges: F:S.90

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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