SMTL ID : 4ysn.1

Structure of aminoacid racemase in complex with PLP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-tetramer

Ligands

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

PLP.1: 14 residues within 4Å: Chain A: S.126, G.127, S.128, N.131, Y.154, H.155, E.229, D.234, D.262, V.264, N.265, K.292 Chain B: F.320, T.321 17 PLIP interactions: 3 interactions with chain B, 14 interactions with chain A Hydrogen bonds: B:T.321, B:T.321, A:S.126, A:G.127, A:S.128, A:D.234, A:N.265 Water bridges: B:A.323, A:S.128, A:S.128, A:D.234, A:K.292 Hydrophobic interactions: A:V.264, A:N.265, A:K.292 Salt bridges: A:K.292 pi-Stacking: A:Y.154 PLP.2: 14 residues within 4Å: Chain A: F.320, T.321 Chain B: S.126, G.127, S.128, N.131, Y.154, H.155, E.229, D.234, D.262, V.264, N.265, K.292 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:E.229, B:V.264, B:N.265, B:K.292 Hydrogen bonds: B:S.126, B:G.127, B:S.128, B:N.265, A:T.321, A:T.321 Water bridges: B:D.234, B:K.292, A:T.322, A:A.323 Salt bridges: B:K.292 pi-Stacking: B:Y.154 PLP.3: 14 residues within 4Å: Chain C: S.126, G.127, S.128, N.131, Y.154, H.155, E.229, D.234, D.262, V.264, N.265, K.292 Chain D: F.320, T.321 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:V.264, C:N.265, C:K.292 Hydrogen bonds: C:G.127, C:S.128, C:D.234, C:N.265, C:K.292, D:T.321, D:T.321 Water bridges: C:Y.154, C:D.234, D:A.323 Salt bridges: C:K.292 pi-Stacking: C:Y.154 PLP.4: 14 residues within 4Å: Chain C: F.320, T.321 Chain D: S.126, G.127, S.128, N.131, Y.154, H.155, E.229, D.234, D.262, V.264, N.265, K.292 17 PLIP interactions: 13 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:E.229, D:V.264, D:N.265, D:K.292 Hydrogen bonds: D:G.127, D:S.128, D:N.265, D:K.292, C:T.321, C:T.321 Water bridges: D:S.128, D:Y.154, D:D.234, C:T.322, C:A.323 Salt bridges: D:K.292 pi-Stacking: D:Y.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hayashi, J. et al., Crystal structure of the novel amino-acid racemase isoleucine 2-epimerase from Lactobacillus buchneri. Acta Crystallogr D Struct Biol (2017)

Release Date

2016-04-20

Peptides

Putative 4-aminobutyrate aminotransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Putative 4-aminobutyrate aminotransferase

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