SMTL ID : 3uav.1

Crystal structure of adenosine phosphorylase from Bacillus cereus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-hexamer

Ligands

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 7 residues within 4Å: Chain A: P.19, G.20, D.21, R.87, G.89, T.90 Chain F: R.43 7 PLIP interactions: 1 interactions with chain F, 6 interactions with chain A Salt bridges: F:R.43, A:R.87 Hydrogen bonds: A:G.20, A:D.21, A:V.88, A:T.90 Water bridges: A:T.90 SO4.2: 5 residues within 4Å: Chain A: T.119 Chain F: R.161, E.162, S.163 Ligands: GOL.4 5 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F, 2 interactions with chain A Water bridges: E:K.169, A:T.119, A:T.119 Hydrogen bonds: F:E.162, F:S.163 SO4.5: 7 residues within 4Å: Chain B: P.19, G.20, D.21, R.87, G.89, T.90 Chain E: R.43 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:G.20, B:D.21, B:V.88, B:T.90 Water bridges: B:T.90 Salt bridges: B:R.87, E:R.43 SO4.6: 5 residues within 4Å: Chain B: T.119 Chain E: R.161, E.162, S.163 Ligands: GOL.8 5 PLIP interactions: 2 interactions with chain E, 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: E:E.162, E:S.163 Water bridges: B:T.119, B:T.119, D:K.169 SO4.9: 7 residues within 4Å: Chain C: P.19, G.20, D.21, R.87, G.89, T.90 Chain D: R.43 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.20, C:D.21, C:V.88, C:T.90 Water bridges: C:T.90 Salt bridges: C:R.87, D:R.43 SO4.10: 5 residues within 4Å: Chain C: T.119 Chain D: R.161, E.162, S.163 Ligands: GOL.12 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D, 1 interactions with chain F Water bridges: C:T.119, C:T.119, F:K.169 Hydrogen bonds: D:E.162, D:S.163 SO4.13: 7 residues within 4Å: Chain C: R.43 Chain D: P.19, G.20, D.21, R.87, G.89, T.90 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.20, D:D.21, D:V.88, D:T.90 Salt bridges: D:R.87, C:R.43 Water bridges: C:R.43 SO4.14: 5 residues within 4Å: Chain C: R.161, E.162, S.163 Chain D: T.119 Ligands: GOL.16 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: C:E.162, C:S.163 Water bridges: D:T.119, B:K.169 SO4.17: 7 residues within 4Å: Chain B: R.43 Chain E: P.19, G.20, D.21, R.87, G.89, T.90 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:G.20, E:D.21, E:V.88, E:T.90 Salt bridges: E:R.87, B:R.43 Water bridges: B:R.43 SO4.18: 5 residues within 4Å: Chain B: R.161, E.162, S.163 Chain E: T.119 Ligands: GOL.20 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: B:E.162, B:S.163 Water bridges: A:K.169, E:T.119 SO4.21: 7 residues within 4Å: Chain A: R.43 Chain F: P.19, G.20, D.21, R.87, G.89, T.90 7 PLIP interactions: 5 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:G.20, F:D.21, F:V.88, F:T.90 Salt bridges: F:R.87, A:R.43 Water bridges: A:R.43 SO4.22: 5 residues within 4Å: Chain A: R.161, E.162, S.163 Chain F: T.119 Ligands: GOL.24 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain F, 1 interactions with chain C Hydrogen bonds: A:E.162, A:S.163 Water bridges: F:T.119, C:K.169

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: S.2, N.74, E.75, Q.78, S.79 Chain F: Y.160 No protein-ligand interaction detected (PLIP) GOL.4: 5 residues within 4Å: Chain A: L.118 Chain F: R.161, S.163, M.166 Ligands: SO4.2 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:R.161, F:R.161 Water bridges: F:S.163, F:M.166, A:L.118 GOL.7: 6 residues within 4Å: Chain B: S.2, N.74, E.75, Q.78, S.79 Chain E: Y.160 No protein-ligand interaction detected (PLIP) GOL.8: 5 residues within 4Å: Chain B: L.118 Chain E: R.161, S.163, M.166 Ligands: SO4.6 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:R.161, E:R.161 Water bridges: E:S.163, E:M.166, B:L.118 GOL.11: 6 residues within 4Å: Chain C: S.2, N.74, E.75, Q.78, S.79 Chain D: Y.160 No protein-ligand interaction detected (PLIP) GOL.12: 5 residues within 4Å: Chain C: L.118 Chain D: R.161, S.163, M.166 Ligands: SO4.10 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.161, D:R.161 Water bridges: D:S.163, D:M.166, C:L.118 GOL.15: 6 residues within 4Å: Chain C: Y.160 Chain D: S.2, N.74, E.75, Q.78, S.79 1 PLIP interactions: 1 interactions with chain C Water bridges: C:Y.160 GOL.16: 5 residues within 4Å: Chain C: R.161, S.163, M.166 Chain D: L.118 Ligands: SO4.14 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Water bridges: D:L.118, C:S.163, C:M.166 Hydrogen bonds: C:R.161, C:R.161 GOL.19: 6 residues within 4Å: Chain B: Y.160 Chain E: S.2, N.74, E.75, Q.78, S.79 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.160 GOL.20: 5 residues within 4Å: Chain B: R.161, S.163, M.166 Chain E: L.118 Ligands: SO4.18 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:R.161, B:R.161 Water bridges: B:S.163, B:M.166, E:L.118 GOL.23: 6 residues within 4Å: Chain A: Y.160 Chain F: S.2, N.74, E.75, Q.78, S.79 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.160 GOL.24: 5 residues within 4Å: Chain A: R.161, S.163, M.166 Chain F: L.118 Ligands: SO4.22 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:R.161, A:R.161 Water bridges: A:S.163, A:M.166, F:L.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dessanti, P. et al., Structural basis of the substrate specificity of Bacillus cereus adenosine phosphorylase. Acta Crystallogr.,Sect.D (2012)

Release Date

2012-02-29

Peptides

Purine nucleoside phosphorylase deoD-type: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Purine nucleoside phosphorylase deoD-type

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