SMTL ID : 1pr5.1

Escherichia coli Purine Nucleoside Phosphorylase Complexed with 7-deazaadenosine and Phosphate/Sulfate

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: 7 residues within 4Å: Chain A: G.21, D.22, R.88, G.90, S.91 Chain D: R.44 Ligands: TBN.2 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.21, A:D.22, A:S.91, A:S.91 Salt bridges: A:R.88, D:R.44 PO4.3: 6 residues within 4Å: Chain B: G.21, R.88, G.90, S.91 Chain F: R.44 Ligands: TBN.4 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:G.21, B:D.22, B:S.91, B:S.91 Salt bridges: B:R.88, F:R.44 PO4.5: 11 residues within 4Å: Chain C: P.20, G.21, D.22, R.25, R.88, V.89, G.90, S.91, E.182 Chain E: R.44 Ligands: TBN.6 6 PLIP interactions: 1 interactions with chain E, 5 interactions with chain C Salt bridges: E:R.44, C:R.25, C:R.88 Hydrogen bonds: C:G.21, C:S.91 Water bridges: C:S.91 PO4.7: 7 residues within 4Å: Chain A: R.44 Chain D: G.21, D.22, R.88, G.90, S.91 Ligands: TBN.8 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:G.21, D:D.22, D:S.91, D:S.91 Salt bridges: D:R.88, A:R.44 PO4.9: 6 residues within 4Å: Chain C: R.44 Chain E: G.21, R.88, G.90, S.91 Ligands: TBN.10 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:G.21, E:D.22, E:S.91, E:S.91 Salt bridges: E:R.88, C:R.44 PO4.11: 11 residues within 4Å: Chain B: R.44 Chain F: P.20, G.21, D.22, R.25, R.88, V.89, G.90, S.91, E.182 Ligands: TBN.12 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:G.21, F:S.91 Water bridges: F:S.91 Salt bridges: F:R.25, F:R.88, B:R.44

6 x TBN: '2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL(Non-covalent)

TBN.2: 15 residues within 4Å: Chain A: M.65, R.88, S.91, C.92, G.93, F.160, V.179, E.180, M.181, E.182, S.204, D.205 Chain D: H.5, R.44 Ligands: PO4.1 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:R.88, A:S.91, A:M.181, A:D.205, D:H.5, D:R.44 TBN.4: 14 residues within 4Å: Chain B: M.65, R.88, S.91, C.92, G.93, F.160, V.179, E.180, M.181, E.182, D.205 Chain F: H.5, R.44 Ligands: PO4.3 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain F Hydrogen bonds: B:R.88, B:S.91, B:M.181, B:D.205, F:H.5, F:R.44 TBN.6: 16 residues within 4Å: Chain C: M.65, R.88, S.91, C.92, G.93, F.160, V.179, E.180, M.181, E.182, S.204, D.205, I.207 Chain E: H.5, R.44 Ligands: PO4.5 7 PLIP interactions: 2 interactions with chain E, 5 interactions with chain C Hydrogen bonds: E:H.5, E:R.44, C:S.91, C:M.181, C:D.205 Hydrophobic interactions: C:F.160 Water bridges: C:S.91 TBN.8: 15 residues within 4Å: Chain A: H.5, R.44 Chain D: M.65, R.88, S.91, C.92, G.93, F.160, V.179, E.180, M.181, E.182, S.204, D.205 Ligands: PO4.7 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:H.5, A:R.44, D:R.88, D:S.91, D:M.181, D:D.205 TBN.10: 14 residues within 4Å: Chain C: H.5, R.44 Chain E: M.65, R.88, S.91, C.92, G.93, F.160, V.179, E.180, M.181, E.182, D.205 Ligands: PO4.9 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:R.88, E:S.91, E:M.181, E:D.205, C:H.5, C:R.44 TBN.12: 16 residues within 4Å: Chain B: H.5, R.44 Chain F: M.65, R.88, S.91, C.92, G.93, F.160, V.179, E.180, M.181, E.182, S.204, D.205, I.207 Ligands: PO4.11 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain F Hydrogen bonds: B:H.5, B:R.44, F:S.91, F:M.181, F:D.205 Hydrophobic interactions: F:F.160 Water bridges: F:S.91

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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