SMTL ID : 7agz.1

BsrV no-histagged

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 14 residues within 4Å: Chain A: I.49, K.51, Y.55, V.97, R.150, M.179, H.181, N.221, S.222, R.237, P.238, G.239, G.240 Ligands: GOL.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.49, A:K.51 Hydrogen bonds: A:Y.55, A:R.150, A:R.150, A:N.221, A:S.222, A:R.237, A:R.237, A:G.239, A:G.240 Water bridges: A:K.51, A:V.97, A:Y.223 pi-Stacking: A:H.181 PLP.4: 12 residues within 4Å: Chain A: Y.276 Chain B: K.51, Y.55, V.97, R.150, H.181, N.221, S.222, R.237, G.239, G.240 Ligands: GOL.5 14 PLIP interactions: 2 interactions with chain A, 12 interactions with chain B Water bridges: A:Y.276, A:N.325, B:Y.185, B:Y.223 Hydrophobic interactions: B:K.51 Hydrogen bonds: B:Y.55, B:R.150, B:R.150, B:N.221, B:S.222, B:R.237, B:G.239, B:G.240 pi-Stacking: B:H.181

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: Y.55, Y.185, D.245, P.368, Y.371 Chain B: M.324 Ligands: PLP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.55, A:Y.185, A:D.245, A:Y.371 Water bridges: A:S.222 GOL.5: 7 residues within 4Å: Chain A: M.324 Chain B: Y.55, Y.185, D.245, P.368, Y.371 Ligands: PLP.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.185, B:Y.185, B:Y.371

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: R.150, N.151, H.181 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain B: R.150, N.151, H.181 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Espaillat, A. et al., Binding of non-canonical peptidoglycan controls Vibrio cholerae broad spectrum racemase activity. Comput Struct Biotechnol J (2021)

Release Date

2021-10-06

Peptides

Broad specificity amino-acid racemase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Broad specificity amino-acid racemase