SMTL ID : 3fuc.1

Recombinant calf purine nucleoside phosphorylase in a binary complex with multisubstrate analogue inhibitor 9-(5',5'-difluoro-5'-phosphonopentyl)-9-deazaguanine structure in a new space group with one full trimer in the asymmetric unit

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-trimer

Ligands

3 x 9D9: [5-(2-amino-4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)-1,1-difluoropentyl]phosphonic acid(Non-covalent)

9D9.1: 19 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, V.245 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.33, A:R.84, A:A.116, A:S.220, A:N.243, A:N.243 Water bridges: A:E.201, A:E.201, A:S.220 Salt bridges: A:E.201 pi-Stacking: A:F.200, A:F.200 9D9.3: 19 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, V.245 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.33, B:R.84, B:A.116, B:S.220, B:N.243, B:N.243 Water bridges: B:E.201, B:E.201, B:S.220 Salt bridges: B:E.201 pi-Stacking: B:F.200 9D9.4: 19 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, V.245 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.33, C:R.84, C:A.116, C:S.220, C:N.243, C:N.243 Water bridges: C:E.201, C:E.201, C:S.220 Salt bridges: C:E.201 pi-Stacking: C:F.200

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: E.186 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.186, H2O.1, H2O.4, H2O.6 MG.5: 2 residues within 4Å: Chain C: D.9, D.12 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.9, H2O.12, H2O.16, H2O.17 MG.6: 1 residues within 4Å: Chain C: E.186 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.186, H2O.16, H2O.16, H2O.16

1 x AZI: AZIDE ION(Non-covalent)

AZI.7: 3 residues within 4Å: Chain C: G.90, P.92, K.95 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.95, C:K.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chojnowski, G. et al., 1.45 A resolution crystal structure of recombinant PNP in complex with a pM multisubstrate analogue inhibitor bearing one feature of the postulated transition state. Biochem.Biophys.Res.Commun. (2010)

Release Date

2009-12-08

Peptides

Purine nucleoside phosphorylase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Purine nucleoside phosphorylase

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