SMTL ID : 2y7g.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 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: AAE.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.52, A:H.54, A:E.236, H2O.11 ZN.6: 5 residues within 4Å: Chain B: H.52, H.54, S.88, E.236 Ligands: AAE.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.52, B:H.54, B:E.236, H2O.20 ZN.8: 5 residues within 4Å: Chain C: H.52, H.54, S.88, E.236 Ligands: AAE.9 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.52, C:H.54, C:E.236, H2O.30 ZN.13: 5 residues within 4Å: Chain D: H.52, H.54, S.88, E.236 Ligands: AAE.14 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.52, D:H.54, D:E.236, H2O.39

4 x AAE: ACETOACETIC ACID(Non-functional Binders)

AAE.2: 13 residues within 4Å: Chain A: H.52, H.54, S.88, T.89, G.90, T.112, N.114, E.149, Y.151, V.178, R.232, E.236 Ligands: ZN.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:E.149, A:V.178 Hydrogen bonds: A:T.89, A:G.90, A:N.114, A:R.232, A:R.232 Salt bridges: A:H.52, A:H.54 AAE.7: 13 residues within 4Å: Chain B: H.52, H.54, S.88, T.89, G.90, T.112, N.114, E.149, Y.151, V.178, R.232, E.236 Ligands: ZN.6 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:E.149, B:V.178 Hydrogen bonds: B:T.89, B:G.90, B:T.112, B:N.114, B:R.232, B:R.232 Salt bridges: B:H.52, B:H.54 AAE.9: 13 residues within 4Å: Chain C: H.52, H.54, S.88, T.89, G.90, T.112, N.114, E.149, Y.151, V.178, R.232, E.236 Ligands: ZN.8 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:E.149, C:V.178 Hydrogen bonds: C:T.89, C:G.90, C:T.112, C:N.114, C:R.232, C:R.232 Salt bridges: C:H.52, C:H.54 AAE.14: 13 residues within 4Å: Chain D: H.52, H.54, S.88, T.89, G.90, T.112, N.114, E.149, Y.151, V.178, R.232, E.236 Ligands: ZN.13 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:E.149, D:V.178 Hydrogen bonds: D:T.89, D:G.90, D:N.114, D:R.232, D:R.232 Salt bridges: D:H.52, D:H.54

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: E.248, S.249, A.251 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.249, A:S.249 Water bridges: A:E.248 GOL.10: 3 residues within 4Å: Chain C: E.248, S.249, A.251 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.248, C:S.249, C:S.249 Water bridges: C:E.248

4 x MG: MAGNESIUM ION(Non-functional Binders)

MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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
A

D
B

3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME

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