SMTL ID : 1pr4.1

Escherichia coli Purine Nucleoside Phosphorylase Complexed with 9-beta-D-ribofuranosyl-6-methylthiopurine and Phosphate/Sulfate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 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: MTP.2 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.21, A:D.22, A:S.91, A:S.91 Water bridges: A:S.91 Salt bridges: A:R.88, D:R.44 PO4.3: 8 residues within 4Å: Chain B: P.20, G.21, R.88, V.89, G.90, S.91 Chain F: R.44 Ligands: MTP.4 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:G.21, B:V.89, B:S.91, B:S.91 Water bridges: B:D.22, B:D.22 Salt bridges: B:R.88, F:R.44 PO4.5: 10 residues within 4Å: Chain C: P.20, G.21, R.25, R.88, V.89, G.90, S.91, E.182 Chain E: R.44 Ligands: MTP.6 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:G.21, C:V.89, C:S.91, C:S.91 Water bridges: C:S.91 Salt bridges: C:R.25, C:R.88, E:R.44 PO4.7: 7 residues within 4Å: Chain A: R.44 Chain D: G.21, D.22, R.88, G.90, S.91 Ligands: MTP.8 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain D Salt bridges: A:R.44, D:R.88 Hydrogen bonds: D:G.21, D:D.22, D:S.91, D:S.91 Water bridges: D:S.91 PO4.9: 8 residues within 4Å: Chain C: R.44 Chain E: P.20, G.21, R.88, V.89, G.90, S.91 Ligands: MTP.10 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:G.21, E:V.89, E:S.91, E:S.91 Water bridges: E:D.22, E:D.22 Salt bridges: E:R.88, C:R.44 PO4.11: 10 residues within 4Å: Chain B: R.44 Chain F: P.20, G.21, R.25, R.88, V.89, G.90, S.91, E.182 Ligands: MTP.12 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain F Salt bridges: B:R.44, F:R.25, F:R.88 Hydrogen bonds: F:G.21, F:V.89, F:S.91, F:S.91 Water bridges: F:S.91

6 x MTP: 2-HYDROXYMETHYL-5-(6-METHYLSULFANYL-PURIN-9-YL)-TETRAHYDRO-FURAN-3,4-DIOL(Non-covalent)

MTP.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, D.205, I.207 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, D:H.5, D:R.44 Water bridges: A:S.204 MTP.4: 15 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, I.207 Chain F: H.5, R.44 Ligands: PO4.3 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:H.5, F:R.44, B:S.91, B:M.181 MTP.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 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:R.88, C:S.91, C:M.181, E:H.5, E:R.44 Water bridges: C:S.91 MTP.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, D.205, I.207 Ligands: PO4.7 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:R.88, D:S.91, D:M.181, A:H.5, A:R.44 Water bridges: D:S.204 MTP.10: 15 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, I.207 Ligands: PO4.9 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:S.91, E:M.181, C:H.5, C:R.44 MTP.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 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain F Hydrogen bonds: B:H.5, B:R.44, F:R.88, F:S.91, F:M.181 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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