SMTL ID : 8zpf.2 (1 other biounit)

SFX reaction state structure (0-20min) of alanine racemase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.1: 13 residues within 4Å: Chain A: V.41, K.43, Y.47, L.89, R.143, H.173, N.213, T.214, R.229, G.231, I.232, Y.368 Ligands: ALA.3 12 PLIP interactions: 3 Ligand-Ligand interactions, 9 interactions with chain A Hydrophobic interactions: A.3, A:L.89 Hydrogen bonds: A.3, A.3, A:K.43, A:R.143, A:T.214, A:R.229, A:G.231, A:I.232, A:Y.368 pi-Stacking: A:H.173 PLP.4: 11 residues within 4Å: Chain B: V.41, K.43, Y.47, R.143, H.173, N.213, T.214, R.229, G.231, I.232, Y.368 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:K.43, B:Y.47, B:R.143, B:N.213, B:T.214, B:T.214, B:R.229, B:G.231, B:I.232, B:Y.368 Water bridges: B:K.43, B:A.215

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

CL.2: 3 residues within 4Å: Chain A: N.136, R.143, L.144 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain B: N.136, R.143, L.144 Ligand excluded by PLIP

1 x ALA: ALANINE(Non-covalent)

ALA.3: 7 residues within 4Å: Chain A: K.43, Y.47, R.143 Chain B: Y.276, T.323, M.324 Ligands: PLP.1 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:M.324 Hydrogen bonds: B:Y.276, B:Y.276, B:M.324 Water bridges: B:T.323, B:D.325 Salt bridges: A:K.43, A:R.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, J. et al., Exploring the reaction dynamics of alanine racemase using serial femtosecond crystallography. Sci Rep (2024)

Release Date

2025-01-01

Peptides

Alanine racemase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Alanine racemase 2

Related Entries With Identical Sequence