SMTL ID : 7d8q.1

The structure of nucleotide phosphatase Sa1684 complex with GDP analogue from Staphylococcus aureus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x GZF: [(2R,3R,4S,5S)-5-(2-azanyl-6-oxidanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl bis(oxidanyl)phosphinothioyl hydrogen phosphate(Non-covalent)

GZF.1: 8 residues within 4Å: Chain A: H.25, R.26, E.52, W.58, Y.88, D.123, E.126 Ligands: MG.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.26, A:R.26, A:Y.88, A:D.110 Salt bridges: A:R.26 pi-Stacking: A:W.58, A:W.58 pi-Cation interactions: A:W.58, A:W.58

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: N.90, D.106, D.110 Ligands: MG.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.106, A:D.110, H2O.1, H2O.2, H2O.2 MG.3: 6 residues within 4Å: Chain A: D.108, D.110, D.123, E.126 Ligands: GZF.1, MG.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.108, A:D.110, A:D.123, A:E.126, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Z. et al., The structural mechanism for the nucleoside tri- and diphosphate hydrolysis activity of Ntdp from Staphylococcus aureus. Febs J. (2021)

Release Date

2021-03-17

Peptides

UPF0374 protein SAB1800c: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UPF0374 protein SAB1800c

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