SMTL ID : 5dqw.1

The crystal structure of Bacillus subtilis YpgQ in complex with ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 7 residues within 4Å: Chain A: H.31, D.68, R.142, A.143, F.146, H.164, L.169 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.142, A:R.142 Water bridges: A:G.30, A:D.130, A:A.143, A:H.152, A:Q.159 Salt bridges: A:H.31, A:H.31 pi-Stacking: A:F.146, A:F.146, A:H.164, A:H.164 ADP.3: 8 residues within 4Å: Chain B: H.31, D.68, D.130, R.142, A.143, F.146, H.164, L.169 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:D.68, B:D.130, B:R.142 Water bridges: B:R.142, B:A.143, B:A.143, B:H.152, B:Q.159 Salt bridges: B:H.31, B:H.31 pi-Stacking: B:F.146, B:H.164, B:H.164

2 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 4 residues within 4Å: Chain A: H.35, H.64, D.65, D.130 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.35, A:H.64, A:D.65, A:D.130, H2O.1 NI.4: 4 residues within 4Å: Chain B: H.35, H.64, D.65, D.130 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.35, B:H.64, B:D.65, B:D.130, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jeon, Y.J. et al., Structural and biochemical characterization of bacterial YpgQ protein reveals a metal-dependent nucleotide pyrophosphohydrolase. J.Struct.Biol. (2016)

Release Date

2016-04-27

Peptides

Uncharacterized protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Uncharacterized protein

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