SMTL ID : 7d8l.1

The structure of nucleoside phosphatase Sa1684 complex with GTP analogue from Staphylococcus aureus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x GSP: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE(Non-covalent)

GSP.1: 14 residues within 4Å: Chain A: H.25, R.26, W.28, N.45, W.58, T.60, E.62, A.64, I.77, M.79, Y.88, D.123, E.126 Ligands: MG.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.26, A:R.26, A:W.28, A:N.45, A:N.45, A:E.62, A:Y.88 Water bridges: A:R.61, A:A.64, A:R.81, A:N.90, A:N.90 Salt bridges: A:R.26, A:R.26 pi-Stacking: 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 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.106, A:D.110, H2O.1, H2O.2 MG.3: 6 residues within 4Å: Chain A: D.108, D.110, D.123, E.126 Ligands: GSP.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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: L.121, Q.152 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.152, A:Q.152

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 SA1684: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UPF0374 protein SA1684

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