SMTL ID : 5tk6.1

Structure of the HD-domain phosphohydrolase OxsA with Oxetanocin-A diphosphate bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: H.31, H.66, D.67, D.132 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.31, A:H.66, A:D.67, A:D.132, H2O.1, H2O.2 MG.2: 2 residues within 4Å: Chain A: D.132 Ligands: 7D3.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.132, H2O.1, H2O.2, H2O.2 MG.4: 4 residues within 4Å: Chain B: H.31, H.66, D.67, D.132 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.31, B:H.66, B:D.67, B:D.132, H2O.4, H2O.5 MG.5: 2 residues within 4Å: Chain B: D.132 Ligands: 7D3.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.132, H2O.4, H2O.5, H2O.5

2 x 7D3: [(2S,3R,4R)-4-(6-amino-9H-purin-9-yl)-3-(hydroxymethyl)oxetan-2-yl]methyl trihydrogen diphosphate(Non-covalent)

7D3.3: 13 residues within 4Å: Chain A: R.16, W.17, H.75, I.77, S.78, P.79, K.82, D.132, A.136, I.154, S.157, L.158 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.17 Hydrogen bonds: A:W.17, A:S.78, A:S.78, A:S.157, A:S.157 Water bridges: A:R.16, A:D.132, A:D.132, A:D.132 Salt bridges: A:K.161, A:K.161 7D3.6: 13 residues within 4Å: Chain B: R.16, W.17, H.75, I.77, S.78, P.79, K.82, D.132, A.136, I.154, S.157, L.158 Ligands: MG.5 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.17 Hydrogen bonds: B:W.17, B:S.78, B:S.78, B:H.133, B:S.157, B:S.157 Water bridges: B:R.16, B:D.132, B:D.132, B:D.132 Salt bridges: B:K.161, B:K.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bridwell-Rabb, J. et al., An HD domain phosphohydrolase active site tailored for oxetanocin-A biosynthesis. Proc. Natl. Acad. Sci. U.S.A. (2016)

Release Date

2016-11-23

Peptides

OxsA protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

OxsA protein

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