SMTL ID : 7xll.1

Alanine racemase from Lactobacillus sakei Uonuma-1.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 6 residues within 4Å: Chain A: K.41, I.135, R.141, I.142, F.170, H.172 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.170, A:H.172 Hydrogen bonds: A:I.142 Salt bridges: A:R.141 ACT.2: 5 residues within 4Å: Chain A: D.136, S.137, R.145, R.190, L.194 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.190 Water bridges: A:R.145 Salt bridges: A:R.145, A:R.190 ACT.3: 7 residues within 4Å: Chain A: G.4, Y.5, R.7, T.9, R.10, P.371, V.373 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.10, A:P.371, A:V.373 Hydrogen bonds: A:T.9 Salt bridges: A:R.10 ACT.6: 5 residues within 4Å: Chain B: S.301, T.302, E.350, L.351, Y.354 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.354 Hydrogen bonds: B:T.302, B:T.302, B:E.350 Water bridges: B:R.309 Salt bridges: B:R.309 ACT.7: 7 residues within 4Å: Chain B: K.41, I.135, M.139, R.141, I.142, F.170, H.172 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.170, B:H.172 Hydrogen bonds: B:I.142 Water bridges: B:R.141 Salt bridges: B:R.141 ACT.8: 5 residues within 4Å: Chain B: D.136, S.137, G.138, R.145, R.190 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.136 Salt bridges: B:R.145, B:R.190

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: E.54, Q.57, A.78, N.79, F.80 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.54, A:Q.57, A:Q.57

1 x ALA: ALANINE(Non-covalent)

ALA.5: 9 residues within 4Å: Chain A: Y.271, Y.290, C.317, M.318 Chain B: K.41, Y.45, R.141, H.172, Y.360 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.271, A:Y.271, A:Y.290, A:M.318 Water bridges: A:D.319, A:Q.320 Hydrophobic interactions: B:Y.360 Salt bridges: B:R.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimizu-Ibuka, A. et al., Regulation of alanine racemase activity by carboxylates and the d-type substrate d-alanine. Febs J. (2023)

Release Date

2023-03-01

Peptides

Alanine racemase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alanine racemase