SMTL ID : 2y7f.1

Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (Kce) from C. Cloacamonas acidaminovorans in complex with the substrate 3- keto-5-aminohexanoate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.52, H.54, S.88, E.236 Ligands: KMH.2 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:H.52, A:H.54, A:E.236, KMH.2, H2O.10 ZN.3: 5 residues within 4Å: Chain B: H.52, H.54, S.88, E.236 Ligands: KMH.4 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:H.52, B:H.54, B:E.236, KMH.4, H2O.18 ZN.5: 5 residues within 4Å: Chain C: H.52, H.54, S.88, E.236 Ligands: KMH.6 5 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: C:H.52, C:H.54, C:E.236, KMH.6, H2O.26 ZN.7: 5 residues within 4Å: Chain D: H.52, H.54, S.88, E.236 Ligands: KMH.8 5 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: D:H.52, D:H.54, D:E.236, KMH.8, H2O.34

4 x KMH: (5S)-5-AMINO-3-OXO-HEXANOIC ACID(Non-covalent)

KMH.2: 14 residues within 4Å: Chain A: E.20, H.52, H.54, S.88, G.90, G.91, V.93, T.112, N.114, F.120, F.125, Y.151, E.236 Ligands: ZN.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.93, A:F.120, A:F.125, A:F.125 Hydrogen bonds: A:E.20, A:G.90, A:T.112, A:N.114, A:N.114 Water bridges: A:R.232, A:R.232 Salt bridges: A:H.52, A:H.54 KMH.4: 14 residues within 4Å: Chain B: E.20, H.52, H.54, S.88, G.90, G.91, V.93, T.112, N.114, F.120, F.125, Y.151, E.236 Ligands: ZN.3 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.93, B:F.120, B:F.125, B:F.125 Hydrogen bonds: B:E.20, B:G.90, B:N.114 Water bridges: B:R.232 Salt bridges: B:H.52, B:H.54 KMH.6: 13 residues within 4Å: Chain C: E.20, H.52, H.54, S.88, G.90, G.91, V.93, T.112, N.114, F.125, Y.151, E.236 Ligands: ZN.5 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:V.93, C:F.125 Hydrogen bonds: C:G.90, C:G.91, C:N.114, C:N.114 Water bridges: C:R.232, C:R.232 Salt bridges: C:H.52, C:H.54 KMH.8: 14 residues within 4Å: Chain D: E.20, H.52, H.54, S.88, G.90, G.91, V.93, T.112, N.114, F.120, F.125, Y.151, E.236 Ligands: ZN.7 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:V.93, D:F.120, D:F.125, D:F.125 Hydrogen bonds: D:G.90, D:G.91, D:T.112, D:N.114 Water bridges: D:R.232 Salt bridges: D:H.52, D:H.54

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 2 residues within 4Å: Chain D: D.67, E.71 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.67, D:E.71, H2O.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bellinzoni, M. et al., 3-Keto-5-Aminohexanoate Cleavage Enzyme: A Common Fold for an Uncommon Claisen-Type Condensation. J.Biol.Chem. (2011)

Release Date

2011-06-01

Peptides

3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME

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