SMTL ID : 1v48.2 (1 other biounit)

Calf spleen purine nucleoside phosphorylase (PNP) binary complex with 9-(5,5-difluoro-5-phosphonopenthyl)guanine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.20 Chain B: H.20 Chain C: H.20 Ligands: ZN.4, ZN.7 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.20, C:H.20, B:H.20, H2O.5, H2O.12 ZN.4: 5 residues within 4Å: Chain A: H.20 Chain B: H.20 Chain C: H.20 Ligands: ZN.1, ZN.7 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.20, C:H.20, B:H.20, H2O.5, H2O.12 ZN.7: 5 residues within 4Å: Chain A: H.20 Chain B: H.20 Chain C: H.20 Ligands: ZN.1, ZN.4 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.20, C:H.20, B:H.20, H2O.5, H2O.12

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.51, F.56 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: S.51, F.56 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain C: S.51, F.56 No protein-ligand interaction detected (PLIP)

3 x HA1: 9-(5,5-DIFLUORO-5-PHOSPHONOPENTYL)GUANINE(Non-covalent)

HA1.3: 17 residues within 4Å: Chain A: G.32, S.33, R.84, H.86, N.115, A.116, A.117, G.118, F.200, E.201, V.217, G.218, M.219, S.220, T.242, N.243, V.245 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.33, A:R.84, A:A.116, A:A.116, A:G.218, A:S.220, A:N.243 Water bridges: A:G.32, A:S.33, A:E.201, A:E.201, A:M.219, A:T.242 Salt bridges: A:E.201 pi-Cation interactions: A:F.200 HA1.6: 17 residues within 4Å: Chain B: G.32, S.33, R.84, H.86, N.115, A.116, A.117, G.118, F.200, E.201, V.217, G.218, M.219, S.220, T.242, N.243, V.245 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.33, B:R.84, B:A.116, B:A.116, B:G.218, B:S.220, B:N.243 Water bridges: B:G.32, B:S.33, B:E.201, B:E.201, B:M.219, B:T.242 Salt bridges: B:E.201 pi-Cation interactions: B:F.200 HA1.9: 17 residues within 4Å: Chain C: G.32, S.33, R.84, H.86, N.115, A.116, A.117, G.118, F.200, E.201, V.217, G.218, M.219, S.220, T.242, N.243, V.245 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:S.33, C:R.84, C:A.116, C:A.116, C:G.218, C:S.220, C:N.243 Water bridges: C:G.32, C:S.33, C:E.201, C:E.201, C:M.219, C:T.242 Salt bridges: C:E.201 pi-Cation interactions: C:F.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luic, M. et al., Calf spleen purine-nucleoside phosphorylase: crystal structure of the binary complex with a potent multisubstrate analogue inhibitor. Acta Crystallogr.,Sect.D (2004)

Release Date

2004-08-03

Peptides

Purine nucleoside phosphorylase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Purine nucleoside phosphorylase

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