SMTL ID : 4rqa.2 (1 other biounit)

Crystal Structure of a Hypoxanthine Phosphoribosyltransferase (target ID NYSGRC-029686) from Staphylococcus aureus (orthorhombic space group)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-tetramer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 11 residues within 4Å: Chain A: E.19, Q.23, D.57, K.60, R.61 Chain B: E.19, Q.23, D.57, K.60, R.61 Ligands: GOL.8 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.19, B:K.60, B:K.60, B:R.61, A:E.19, A:K.60, A:R.61 Water bridges: A:Q.23 GOL.2: 4 residues within 4Å: Chain A: E.28, L.29, V.150, G.151 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.28, A:V.150, A:G.151 Water bridges: A:V.150 GOL.8: 11 residues within 4Å: Chain A: E.19, Q.23, D.57, K.60, R.61 Chain B: E.19, Q.23, D.57, K.60, R.61 Ligands: GOL.1 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.19, B:K.60, B:R.61, A:E.19, A:K.60, A:K.60, A:R.61 Water bridges: B:Q.23 GOL.9: 4 residues within 4Å: Chain B: E.28, L.29, V.150, G.151 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.28, B:V.150, B:G.151 Water bridges: B:V.150 GOL.15: 11 residues within 4Å: Chain C: E.19, Q.23, D.57, K.60, R.61 Chain D: E.19, Q.23, D.57, K.60, R.61 Ligands: GOL.22 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:E.19, C:E.19, C:K.60, C:R.61, D:E.19, D:E.19, D:K.60, D:K.60, D:R.61 Water bridges: C:Q.23 GOL.16: 4 residues within 4Å: Chain C: E.28, L.29, V.150, G.151 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.28, C:V.150, C:G.151 Water bridges: C:V.150 GOL.22: 11 residues within 4Å: Chain C: E.19, Q.23, D.57, K.60, R.61 Chain D: E.19, Q.23, D.57, K.60, R.61 Ligands: GOL.15 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:E.19, C:E.19, C:K.60, C:K.60, C:R.61, D:E.19, D:E.19, D:K.60, D:R.61 Water bridges: D:Q.23 GOL.23: 4 residues within 4Å: Chain D: E.28, L.29, V.150, G.151 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.28, D:V.150, D:G.151 Water bridges: D:V.150

4 x NA: SODIUM ION(Non-functional Binders)

NA.3: 9 residues within 4Å: Chain A: S.56, D.57, K.60 Chain B: S.56, D.57, K.60 Ligands: CL.7, NA.10, CL.14 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.57, A:K.60, B:K.60 NA.10: 9 residues within 4Å: Chain A: S.56, D.57, K.60 Chain B: S.56, D.57, K.60 Ligands: NA.3, CL.7, CL.14 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.60, B:D.57, B:K.60 NA.17: 9 residues within 4Å: Chain C: S.56, D.57, K.60 Chain D: S.56, D.57, K.60 Ligands: CL.21, NA.24, CL.28 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:K.60, C:K.60, C:K.60 NA.24: 9 residues within 4Å: Chain C: S.56, D.57, K.60 Chain D: S.56, D.57, K.60 Ligands: NA.17, CL.21, CL.28 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.60, D:K.60, C:K.60

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 5 residues within 4Å: Chain A: L.48, K.49, G.50, D.165, R.171 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:K.49 Hydrogen bonds: A:L.48, A:K.49, A:G.50 Water bridges: A:S.51, A:D.165, A:R.171 Salt bridges: A:R.171 ACT.11: 5 residues within 4Å: Chain B: L.48, K.49, G.50, D.165, R.171 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:K.49 Hydrogen bonds: B:L.48, B:K.49, B:G.50 Water bridges: B:S.51, B:D.165, B:R.171 Salt bridges: B:R.171 ACT.18: 5 residues within 4Å: Chain C: L.48, K.49, G.50, D.165, R.171 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:K.49 Hydrogen bonds: C:L.48, C:K.49, C:G.50 Water bridges: C:S.51, C:R.171 Salt bridges: C:R.171 ACT.25: 5 residues within 4Å: Chain D: L.48, K.49, G.50, D.165, R.171 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:K.49 Hydrogen bonds: D:L.48, D:K.49, D:G.50 Water bridges: D:S.51, D:R.171 Salt bridges: D:R.171

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain A: E.109, K.137, F.158, V.159 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: L.42, S.67, K.99 Ligand excluded by PLIP CL.7: 8 residues within 4Å: Chain A: M.53, D.57, Y.162 Chain B: S.56, D.57, K.60 Ligands: NA.3, NA.10 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: E.109, K.137, F.158, V.159 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: L.42, S.67, K.99 Ligand excluded by PLIP CL.14: 8 residues within 4Å: Chain A: S.56, D.57, K.60 Chain B: M.53, D.57, Y.162 Ligands: NA.3, NA.10 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain C: E.109, K.137, F.158, V.159 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain C: L.42, S.67, K.99 Ligand excluded by PLIP CL.21: 8 residues within 4Å: Chain C: M.53, D.57, Y.162 Chain D: S.56, D.57, K.60 Ligands: NA.17, NA.24 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain D: E.109, K.137, F.158, V.159 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain D: L.42, S.67, K.99 Ligand excluded by PLIP CL.28: 8 residues within 4Å: Chain C: S.56, D.57, K.60 Chain D: M.53, D.57, Y.162 Ligands: NA.17, NA.24 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, A. et al., Crystal Structure of a Hypoxanthine Phosphoribosyltransferase (target ID NYSGRC-029686) from Staphylococcus aureus (orthorhombic space group). To be Published

Release Date

2014-11-26

Peptides

Hypoxanthine phosphoribosyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Hypoxanthine phosphoribosyltransferase

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