SMTL ID : 1lvu.1

Crystal structure of calf spleen purine nucleoside phosphorylase in a new space group with full trimer in the asymmetric unit

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-hexamer

Ligands

10 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: S.51, E.58 Chain D: E.58 Ligands: CA.10 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.51, A:E.58, H2O.1, H2O.1, H2O.4 CA.2: 2 residues within 4Å: Chain A: E.8 Chain E: E.8 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: E:E.8, A:E.8, H2O.3, H2O.4, H2O.57 CA.4: 4 residues within 4Å: Chain B: S.51, E.58 Chain F: E.58 Ligands: CA.14 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.51, B:E.58, H2O.11, H2O.12, H2O.12 CA.5: 1 residues within 4Å: Chain B: D.215 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.215, B:D.215, H2O.11, H2O.19, H2O.23 CA.6: 2 residues within 4Å: Chain B: E.8 Chain D: E.8 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: B:E.8, D:E.8, H2O.11, H2O.15, H2O.35, H2O.38 CA.8: 4 residues within 4Å: Chain C: S.51, E.58 Chain E: E.58 Ligands: CA.12 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:S.51, C:E.58, H2O.23, H2O.25, H2O.49 CA.10: 4 residues within 4Å: Chain A: E.58 Chain D: S.51, E.58 Ligands: CA.1 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:S.51, D:E.58, H2O.35, H2O.35, H2O.39 CA.12: 4 residues within 4Å: Chain C: E.58 Chain E: S.51, E.58 Ligands: CA.8 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:S.51, E:E.58, H2O.48, H2O.49, H2O.50 CA.14: 4 residues within 4Å: Chain B: E.58 Chain F: S.51, E.58 Ligands: CA.4 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:S.51, F:E.58, H2O.13, H2O.60, H2O.61 CA.15: 3 residues within 4Å: Chain F: N.121, R.210, D.215 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.215, F:D.215, H2O.60, H2O.63

6 x 9PP: 2,6-DIAMINO-(S)-9-[2-(PHOSPHONOMETHOXY)PROPYL]PURINE(Non-covalent)

9PP.3: 17 residues within 4Å: Chain A: G.32, S.33, H.86, N.115, A.116, A.117, G.118, L.195, F.200, E.201, V.217, G.218, M.219, S.220, N.243, V.245 Chain B: F.159 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.33, A:A.116, A:A.116, A:S.220, A:N.243, A:N.243 Water bridges: A:H.86, A:Y.88, A:E.201, A:M.219, A:M.219 Salt bridges: A:E.201 pi-Stacking: A:F.200 pi-Cation interactions: A:F.200 Hydrophobic interactions: B:F.159 9PP.7: 18 residues within 4Å: Chain B: G.32, S.33, R.84, H.86, N.115, A.116, A.117, G.118, L.195, F.200, E.201, V.217, G.218, M.219, S.220, N.243, V.245 Chain C: F.159 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.33, B:R.84, B:A.116, B:A.116, B:S.220, B:N.243, B:N.243 Water bridges: B:H.86, B:Y.88, B:E.201, B:M.219, B:M.219, B:M.219 Salt bridges: B:E.201 pi-Stacking: B:F.200 pi-Cation interactions: B:F.200 Hydrophobic interactions: C:F.159 9PP.9: 16 residues within 4Å: Chain A: F.159 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, N.243 18 PLIP interactions: 1 interactions with chain A, 17 interactions with chain C Hydrophobic interactions: A:F.159 Hydrogen bonds: C:S.33, C:R.84, C:A.116, C:A.116, C:S.220, C:N.243, C:N.243 Water bridges: C:H.86, C:N.199, C:E.201, C:M.219, C:M.219, C:M.219, C:M.219 Salt bridges: C:E.201 pi-Stacking: C:F.200 pi-Cation interactions: C:F.200 9PP.11: 16 residues within 4Å: Chain D: G.32, S.33, H.86, N.115, A.116, A.117, G.118, L.195, F.200, E.201, V.217, G.218, M.219, S.220, N.243 Chain E: F.159 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:S.33, D:A.116, D:A.116, D:S.220, D:N.243, D:N.243 Water bridges: D:S.33, D:H.86, D:H.86, D:H.86, D:E.201, D:E.201, D:M.219 Salt bridges: D:E.201 pi-Stacking: D:F.200 pi-Cation interactions: D:F.200 Hydrophobic interactions: E:F.159 9PP.13: 18 residues within 4Å: Chain E: G.32, S.33, R.84, H.86, N.115, A.116, A.117, G.118, L.195, F.200, E.201, V.217, G.218, M.219, S.220, N.243, V.245 Chain F: F.159 19 PLIP interactions: 18 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:S.33, E:R.84, E:A.116, E:A.116, E:S.220, E:N.243, E:N.243 Water bridges: E:S.33, E:H.86, E:H.86, E:N.199, E:E.201, E:M.219, E:M.219, E:M.219 Salt bridges: E:E.201 pi-Stacking: E:F.200 pi-Cation interactions: E:F.200 Hydrophobic interactions: F:F.159 9PP.16: 16 residues within 4Å: Chain D: F.159 Chain F: G.32, S.33, H.86, N.115, A.116, A.117, G.118, L.195, F.200, E.201, V.217, G.218, M.219, S.220, N.243 17 PLIP interactions: 16 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:S.33, F:A.116, F:A.116, F:S.220, F:N.243, F:N.243 Water bridges: F:S.33, F:H.86, F:H.86, F:E.201, F:M.219, F:M.219, F:M.219 Salt bridges: F:E.201 pi-Stacking: F:F.200 pi-Cation interactions: F:F.200 Hydrophobic interactions: D:F.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bzowska, A. et al., Crystal structure of calf spleen purine nucleoside phosphorylase with two full trimers in the asymmetric unit: important implications for the mechanism of catalysis. J.Mol.Biol. (2004)

Release Date

2003-09-02

Peptides

Purine nucleoside phosphorylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Purine nucleoside phosphorylase

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