SMTL ID : 7dg7.1

DPBB domain of VCP-like ATPase from Methanopyrus kandleri

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.1: 4 residues within 4Å: Chain A: E.13, V.82, G.83 Ligands: ZN.7 No protein-ligand interaction detected (PLIP) IMD.2: 6 residues within 4Å: Chain A: Y.16, E.18, K.59, E.61 Ligands: ZN.3, ZN.4 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.59 pi-Stacking: A:Y.16

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 2 residues within 4Å: Chain A: E.18 Ligands: IMD.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.18, H2O.3 ZN.4: 2 residues within 4Å: Chain A: E.61 Ligands: IMD.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.61, A:E.61, H2O.1, H2O.1 ZN.5: 1 residues within 4Å: Chain A: E.39 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.39, H2O.3 ZN.6: 4 residues within 4Å: Chain A: K.22, R.23, D.71, E.74 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.22, A:D.71, A:D.71, A:E.74, H2O.3 ZN.7: 2 residues within 4Å: Chain A: E.13 Ligands: IMD.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.13, A:E.13, H2O.2 ZN.8: 1 residues within 4Å: Chain A: K.9 No protein-ligand interaction detected (PLIP) ZN.9: 1 residues within 4Å: Chain A: E.84 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.84, A:E.84, H2O.1, H2O.2 ZN.10: 2 residues within 4Å: Chain A: S.38, D.41 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.41, A:D.41, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yagi, S. et al., Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase. J.Am.Chem.Soc. (2021)

Release Date

2021-09-29

Peptides

ATPase of the AAA+ class: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ATPase of the AAA+ class