SMTL ID : 3dxw.1

The crystal structure of alpha-amino-epsilon-caprolactam racemase from Achromobacter obae complexed with epsilon caprolactam

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 16 residues within 4Å: Chain A: S.125, G.126, S.127, N.130, Y.153, H.154, G.155, E.221, S.225, D.254, V.256, K.257, K.283 Chain B: Q.310, T.311 Ligands: ICC.2 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:V.256, A:K.283 Hydrogen bonds: A:G.126, A:S.127, A:N.130, A:K.283, B:Q.310, B:T.311, B:T.311 Water bridges: A:H.124, A:S.127, A:S.127 Salt bridges: A:K.283 pi-Stacking: A:Y.153 PLP.3: 15 residues within 4Å: Chain A: Q.310, T.311 Chain B: S.125, G.126, S.127, N.130, Y.153, H.154, E.221, S.225, D.254, V.256, K.257, K.283 Ligands: ICC.4 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.256, B:K.283 Hydrogen bonds: B:G.126, B:S.127, B:S.225, B:K.257, B:K.283, B:K.283, A:T.311 Water bridges: B:H.124, B:S.127, B:S.127 Salt bridges: B:K.283 pi-Stacking: B:Y.153

2 x ICC: azepan-2-one(Non-covalent)

ICC.2: 9 residues within 4Å: Chain A: L.35, W.65, Y.153, K.257, K.283, W.452 Chain B: L.94, T.311 Ligands: PLP.1 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.35, A:W.65, A:W.452, B:L.94 Hydrogen bonds: A:K.257, A:K.283, A:K.283 ICC.4: 8 residues within 4Å: Chain A: L.94, T.311 Chain B: L.35, W.65, K.257, K.283, W.452 Ligands: PLP.3 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.35, B:W.65, B:W.452, A:L.94 Hydrogen bonds: B:K.257, B:K.283

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Okazaki, S. et al., The novel structure of a pyridoxal 5'-phosphate-dependent fold-type I racemase, alpha-amino-epsilon-caprolactam racemase from Achromobacter obae. Biochemistry (2009)

Release Date

2009-07-28

Peptides

Alpha-amino-epsilon-caprolactam racemase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alpha-amino-epsilon-caprolactam racemase