SMTL ID : 5mvr.1

Crystal structure of Bacillus subtilus YdiB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

monomer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: T.12, V.13, N.14, P.15, T.18, D.40, L.41, G.42, A.43, G.44, K.45, T.46, T.47, D.134, R.136 Ligands: MG.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:T.12, A:T.12, A:T.18, A:G.42, A:A.43, A:G.44, A:K.45, A:T.46, A:T.46, A:T.47, A:T.47 Water bridges: A:K.45, A:K.45 Salt bridges: A:K.45 pi-Cation interactions: A:R.136

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.46, E.110 Ligands: ADP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.46, A:E.110

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: K.6, Q.7, L.8 No protein-ligand interaction detected (PLIP) EDO.4: 1 residues within 4Å: Chain A: S.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.2 EDO.5: 2 residues within 4Å: Chain A: Q.125, V.143 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, H.A. et al., Expanding the Kinome World: A New Protein Kinase Family Widely Conserved in Bacteria. J. Mol. Biol. (2017)

Release Date

2017-09-20

Peptides

tRNA threonylcarbamoyladenosine biosynthesis protein TsaE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

tRNA threonylcarbamoyladenosine biosynthesis protein TsaE