SMTL ID : 5y6u.1

Crystal structure of wild-type YabJ protein from Bacillus subtilis (natto).

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-trimer

Ligands

6 x ACY: ACETIC ACID(Non-functional Binders)

ACY.1: 3 residues within 4Å: Chain A: T.2, V.23, N.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.2, A:N.24 ACY.2: 4 residues within 4Å: Chain A: H.9, S.55, K.58, A.59 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.62 ACY.3: 4 residues within 4Å: Chain A: R.109, P.111, K.112 Chain C: M.81 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Water bridges: C:F.84 Hydrogen bonds: A:K.112 ACY.4: 4 residues within 4Å: Chain A: L.123 Chain B: T.2, V.23, N.24 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.2, B:N.24 Hydrophobic interactions: A:L.123 ACY.5: 3 residues within 4Å: Chain B: K.8, H.9, P.37 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.9 ACY.6: 3 residues within 4Å: Chain C: K.8, H.9, P.37 3 PLIP interactions: 3 interactions with chain C Water bridges: C:S.38, C:S.38 Salt bridges: C:H.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fujimoto, Z. et al., Tetramer formation of Bacillus subtilis YabJ protein that belongs to YjgF/YER057c/UK114 family. Biosci.Biotechnol.Biochem. (2021)

Release Date

2018-08-15

Peptides

YabJ protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

YabJ protein