SMTL ID : 7cmj.1

Crystal structure of L.donovani Hypoxanthine-guanine phosphoribosyl transferase (HGPRT)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.76 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.185 Ligands: PO4.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.185, H2O.1, H2O.1, H2O.1 MG.6: 2 residues within 4Å: Chain B: D.185 Ligands: PO4.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.185, H2O.3, H2O.4, H2O.4 MG.12: 2 residues within 4Å: Chain C: D.185 Ligands: PO4.14 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.185, H2O.5, H2O.5, H2O.6 MG.17: 2 residues within 4Å: Chain D: D.185 Ligands: PO4.19 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.185, H2O.7, H2O.8, H2O.8

4 x BA: BARIUM ION(Non-covalent)

BA.2: 2 residues within 4Å: Chain A: E.125, D.126 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.125, A:D.126, H2O.1, H2O.1 BA.7: 3 residues within 4Å: Chain B: E.125, D.126, I.127 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.125, B:D.126, H2O.3, H2O.3 BA.13: 2 residues within 4Å: Chain C: E.125, D.126 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.125, C:D.126, H2O.5, H2O.5 BA.18: 3 residues within 4Å: Chain D: E.125, D.126, I.127 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.125, D:D.126, H2O.7, H2O.7

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 7 residues within 4Å: Chain A: L.65, K.66, G.67, D.185, R.191 Chain B: R.113 Ligands: MG.1 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.66, A:G.67 Salt bridges: A:R.191, B:R.113 PO4.8: 8 residues within 4Å: Chain A: R.113 Chain B: L.65, K.66, G.67, D.126, D.185, R.191 Ligands: MG.6 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.65, B:K.66, B:G.67 Water bridges: B:D.185, B:E.188, B:R.191, B:R.191 Salt bridges: B:R.191, A:R.113 PO4.14: 7 residues within 4Å: Chain C: L.65, K.66, G.67, D.185, R.191 Chain D: R.113 Ligands: MG.12 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Salt bridges: D:R.113, C:R.191 Hydrogen bonds: C:K.66, C:G.67 PO4.19: 8 residues within 4Å: Chain C: R.113 Chain D: L.65, K.66, G.67, D.126, D.185, R.191 Ligands: MG.17 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:L.65, D:K.66, D:G.67 Water bridges: D:D.185, D:E.188, D:R.191, D:R.191 Salt bridges: D:R.191, C:R.113

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 6 residues within 4Å: Chain A: R.113 Chain B: C.92, A.93, S.94, S.95 Chain C: R.107 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: C:R.107, C:R.107, B:S.95, A:R.113 Water bridges: B:A.93 PEG.5: 7 residues within 4Å: Chain A: C.92, A.93, S.94, S.95, L.109 Chain B: R.113 Chain D: R.107 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: D:R.107, D:R.107, B:R.113, A:S.95 PEG.15: 6 residues within 4Å: Chain A: R.107 Chain C: R.113 Chain D: C.92, A.93, S.94, S.95 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: A:R.107, A:R.107, C:R.113, D:S.95 Water bridges: D:A.93 PEG.16: 7 residues within 4Å: Chain B: R.107 Chain C: C.92, A.93, S.94, S.95, L.109 Chain D: R.113 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: C:S.95, B:R.107, B:R.107, D:R.113

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.9: 10 residues within 4Å: Chain A: W.34, D.74, R.77, F.78, R.194 Chain B: W.34, D.74, R.77, F.78, R.194 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.194, B:R.194, A:R.77, A:R.77, A:R.194, A:R.194 PG4.20: 10 residues within 4Å: Chain C: W.34, D.74, R.77, F.78, R.194 Chain D: W.34, D.74, R.77, F.78, R.194 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.77, C:R.77, C:R.194, C:R.194, D:R.194, D:R.194

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

CL.10: 1 residues within 4Å: Chain B: T.26 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: I.172, T.173 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain D: T.26 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain D: I.172, T.173 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parihar, P.S. et al., The L.donovani Hypoxanthine-guanine phosphoribosyl transferase (HGPRT) oligomer is distinct from the human homolog. Biochem.Biophys.Res.Commun. (2020)

Release Date

2021-08-04

Peptides

Hypoxanthine phosphoribosyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Hypoxanthine phosphoribosyltransferase