SMTL ID : 5m49.1

Alpha-amino epsilon-caprolactam racemase in complex with PLP and D/L alpha amino epsilon-caprolactam (internal aldimine)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 17 residues within 4Å: Chain A: S.109, G.110, S.111, N.114, Y.137, H.138, G.139, E.205, S.209, D.238, V.240, K.241, K.267 Chain B: Q.294, T.295 Ligands: 8F4.2, 7F4.3 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:V.240, A:K.267 Hydrogen bonds: A:S.109, A:G.110, A:S.111, A:N.114, B:T.295, B:T.295 Water bridges: A:S.209, B:L.296 Salt bridges: A:K.267 pi-Stacking: A:Y.137 PLP.4: 17 residues within 4Å: Chain A: Q.294, T.295 Chain B: S.109, G.110, S.111, N.114, Y.137, H.138, G.139, E.205, S.209, D.238, V.240, K.241, K.267 Ligands: 8F4.5, 7F4.6 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.240, B:K.267 Hydrogen bonds: B:S.109, B:G.110, B:S.111, B:N.114, A:T.295, A:T.295, A:T.295 Water bridges: B:S.209, A:L.296 Salt bridges: B:K.267 pi-Stacking: B:Y.137

2 x 8F4: (3~{S})-3-azanylazepan-2-one(Non-covalent)

8F4.2: 11 residues within 4Å: Chain A: L.19, W.49, Y.137, D.210, K.241, K.267, W.436 Chain B: L.78, T.295 Ligands: PLP.1, 7F4.3 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.19, A:Y.137, A:W.436, B:L.78 Hydrogen bonds: A:D.210, A:K.241 8F4.5: 11 residues within 4Å: Chain A: L.78, T.295 Chain B: L.19, W.49, Y.137, D.210, K.241, K.267, W.436 Ligands: PLP.4, 7F4.6 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.19, B:Y.137, B:W.436, A:L.78 Hydrogen bonds: B:D.210, B:K.241, B:K.267 Water bridges: B:D.210

2 x 7F4: (3~{R})-3-azanylazepan-2-one(Non-covalent)

7F4.3: 12 residues within 4Å: Chain A: L.19, W.49, Y.137, D.210, K.241, K.267, W.436 Chain B: L.78, M.293, T.295 Ligands: PLP.1, 8F4.2 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.19, A:W.49, A:Y.137, A:W.436, B:L.78 Hydrogen bonds: A:D.210, A:K.241 7F4.6: 12 residues within 4Å: Chain A: L.78, M.293, T.295 Chain B: L.19, W.49, Y.137, D.210, K.241, K.267, W.436 Ligands: PLP.4, 8F4.5 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.19, B:W.49, B:Y.137, B:W.436, A:L.78 Hydrogen bonds: B:D.210, B:K.241, B:K.267 Water bridges: B:D.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Frese, A. et al., Snapshots of the Catalytic Cycle of the Industrial Enzyme alpha-Amino-epsilon-Caprolactam Racemase (ACLR) Observed Using X-ray Crystallography. Acs Catalysis (2017)

Release Date

2017-04-19

Peptides

Aminotransferase class-III: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Aminotransferase class-III