SMTL ID : 5knx.1 (1 other biounit)

Crystal structure of E. coli hypoxanthine phosphoribosyltransferase in complexed with {[(2-[(Hypoxanthin-9H-yl)methyl]propane-1,3-diyl)bis(oxy)]bis- (methylene)}diphosphonic Acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x 6WC: [2-[(6-oxidanylidene-1~{H}-purin-9-yl)methyl]-3-(phosphonomethoxy)propoxy]methylphosphonic acid(Non-covalent)

6WC.1: 16 residues within 4Å: Chain A: S.73, E.103, I.105, I.106, D.107, S.108, G.109, N.110, T.111, K.135, R.138, E.155, F.156, V.157, I.162, D.163 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.73, A:S.73, A:I.105, A:D.107, A:D.107, A:G.109, A:N.110, A:T.111, A:K.135, A:R.138, A:V.157, A:V.157 Water bridges: A:R.47, A:R.47, A:R.47, A:D.163, A:D.163, A:R.169 6WC.3: 16 residues within 4Å: Chain B: S.73, Y.74, I.105, I.106, D.107, S.108, G.109, N.110, T.111, K.135, E.155, F.156, V.157, I.162, D.163 Ligands: MG.5 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:D.107, B:S.108, B:S.108, B:G.109, B:N.110, B:T.111, B:K.135, B:V.157, B:V.157, B:D.163 Water bridges: B:T.111, B:D.163, B:D.163 pi-Stacking: B:F.156 6WC.6: 16 residues within 4Å: Chain C: S.73, E.103, I.105, I.106, D.107, S.108, G.109, N.110, T.111, K.135, R.138, E.155, F.156, V.157, I.162, D.163 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:S.73, C:S.73, C:I.105, C:D.107, C:D.107, C:G.109, C:N.110, C:T.111, C:K.135, C:R.138, C:V.157, C:V.157 Water bridges: C:R.47, C:R.47, C:R.47, C:T.111, C:D.163, C:R.169, C:R.169 6WC.8: 16 residues within 4Å: Chain D: S.73, Y.74, I.105, I.106, D.107, S.108, G.109, N.110, T.111, K.135, E.155, F.156, V.157, I.162, D.163 Ligands: MG.10 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:D.107, D:D.107, D:S.108, D:S.108, D:G.109, D:N.110, D:T.111, D:K.135, D:V.157, D:V.157, D:D.163 Water bridges: D:D.163, D:D.163 pi-Stacking: D:F.156

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.103, D.104 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.103, A:D.104, H2O.3, H2O.3, H2O.3 MG.4: 3 residues within 4Å: Chain B: G.48, E.103, D.104 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: D.163 Ligands: 6WC.3 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain C: E.103, D.104 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.103, C:D.104, H2O.11, H2O.11, H2O.11 MG.9: 3 residues within 4Å: Chain D: G.48, E.103, D.104 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain D: D.163 Ligands: 6WC.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eng, W.S. et al., Crystal Structures of Acyclic Nucleoside Phosphonates in Complex with Escherichia coli Hypoxanthine Phosphoribosyltransferase. Chemistryselect (2016)

Release Date

2017-07-19

Peptides

Hypoxanthine-guanine phosphoribosyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Hypoxanthine-guanine phosphoribosyltransferase

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