SMTL ID : 2ai1.2 (1 other biounit)

Purine nucleoside phosphorylase from calf spleen

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: F.56 Chain B: E.22 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: F.56 Chain C: E.22 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain A: E.22 Chain C: F.56 No protein-ligand interaction detected (PLIP)

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.20 Chain B: H.20 Chain C: H.20 Ligands: ZN.6, ZN.10 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:H.20, B:H.20, A:H.20, H2O.5, H2O.10 ZN.6: 5 residues within 4Å: Chain A: H.20 Chain B: H.20 Chain C: H.20 Ligands: ZN.2, ZN.10 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:H.20, B:H.20, A:H.20, H2O.5, H2O.10 ZN.10: 5 residues within 4Å: Chain A: H.20 Chain B: H.20 Chain C: H.20 Ligands: ZN.2, ZN.6 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:H.20, B:H.20, A:H.20, H2O.5, H2O.10

3 x 144: TRIS-HYDROXYMETHYL-METHYL-AMMONIUM(Non-covalent)

144.3: 5 residues within 4Å: Chain A: E.52 Chain B: E.52 Chain C: E.52 Ligands: 144.7, 144.11 10 PLIP interactions: 3 interactions with chain B, 5 interactions with chain C, 2 interactions with chain A Water bridges: B:E.52, B:E.52, C:T.47, C:E.52, C:E.52, A:E.52 Salt bridges: B:E.52, C:E.52, A:E.52 Hydrogen bonds: C:E.52 144.7: 5 residues within 4Å: Chain A: E.52 Chain B: E.52 Chain C: E.52 Ligands: 144.3, 144.11 10 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: A:E.52 Water bridges: A:T.47, A:E.52, A:E.52, B:E.52, C:E.52, C:E.52 Salt bridges: A:E.52, B:E.52, C:E.52 144.11: 5 residues within 4Å: Chain A: E.52 Chain B: E.52 Chain C: E.52 Ligands: 144.3, 144.7 10 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: B:E.52 Water bridges: B:T.47, B:E.52, B:E.52, C:E.52, A:E.52, A:E.52 Salt bridges: B:E.52, C:E.52, A:E.52

3 x P1G: ((2R,4R,6R,6AS)-4-(2-AMINO-6-OXO-1,6-DIHYDROPURIN-9-YL)-6-(HYDROXYMETHYL)-TETRAHYDROFURO[3,4-D][1,3]DIOXOL-2-YL)METHYLPHOSPHONIC ACID(Non-covalent)

P1G.4: 20 residues within 4Å: Chain A: G.32, S.33, R.84, H.86, Y.88, N.115, A.116, A.117, G.118, L.195, F.200, E.201, V.217, G.218, M.219, S.220, T.242, N.243, H.257, V.260 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.33, A:S.33, A:R.84, A:R.84, A:Y.88, A:A.116, A:G.218, A:M.219, A:S.220, A:T.242, A:N.243 Water bridges: A:E.201, A:E.201, A:S.220, A:S.220 Salt bridges: A:H.86, A:E.201 pi-Stacking: A:F.200 P1G.8: 20 residues within 4Å: Chain B: G.32, S.33, R.84, H.86, Y.88, N.115, A.116, A.117, G.118, L.195, F.200, E.201, V.217, G.218, M.219, S.220, T.242, N.243, H.257, V.260 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:S.33, B:S.33, B:R.84, B:R.84, B:A.116, B:G.218, B:M.219, B:S.220, B:N.243, B:H.257 Water bridges: B:E.201, B:E.201, B:S.220, B:S.220 Salt bridges: B:H.86, B:E.201 pi-Stacking: B:F.200 P1G.12: 20 residues within 4Å: Chain C: G.32, S.33, R.84, H.86, Y.88, N.115, A.116, A.117, G.118, L.195, F.200, E.201, V.217, G.218, M.219, S.220, T.242, N.243, H.257, V.260 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:S.33, C:S.33, C:R.84, C:R.84, C:A.116, C:G.218, C:M.219, C:S.220, C:N.243 Water bridges: C:E.201, C:E.201, C:S.220, C:S.220 Salt bridges: C:H.86, C:E.201 pi-Stacking: C:F.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Toms, A.V. et al., Novel multisubstrate inhibitors of mammalian purine nucleoside phosphorylase. Acta Crystallogr.,Sect.D (2005)

Release Date

2005-10-25

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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