SMTL ID : 8rip.1

Beta-keto acid cleavage enzyme from Paracoccus denitrificans with bound malonate and Coenzyme A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-tetramer

Ligands

4 x MLI: MALONATE ION(Non-functional Binders)

MLI.1: 12 residues within 4Å: Chain A: H.73, H.75, T.109, G.111, S.134, N.136, E.195, Y.197, R.278, E.282 Ligands: COA.2, ZN.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.109, A:G.111, A:S.134, A:N.136, A:N.136, A:E.195 Salt bridges: A:H.73, A:H.73, A:H.75, A:R.278 MLI.4: 12 residues within 4Å: Chain B: H.73, H.75, T.109, G.111, S.134, N.136, E.195, Y.197, R.278, E.282 Ligands: COA.5, ZN.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.109, B:G.111, B:S.134, B:N.136 Salt bridges: B:H.73, B:H.73, B:H.75, B:R.278 MLI.7: 11 residues within 4Å: Chain C: H.73, H.75, T.109, G.111, S.134, N.136, E.195, Y.197, R.278, E.282 Ligands: ZN.8 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:T.110, C:G.111, C:S.134, C:N.136, C:N.136, C:E.195 Salt bridges: C:H.73, C:H.73, C:H.75, C:R.278 MLI.9: 11 residues within 4Å: Chain D: H.73, H.75, T.109, G.111, S.134, N.136, E.195, Y.197, R.278, E.282 Ligands: ZN.10 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.111, D:S.134, D:N.136, D:E.195 Salt bridges: D:H.73, D:H.73, D:H.75, D:R.278

2 x COA: COENZYME A(Non-covalent)

COA.2: 21 residues within 4Å: Chain A: I.41, H.42, F.142, M.147, R.150, Y.151, Y.197, L.226, L.257, A.259, G.260, R.261, E.282, D.283, W.286, G.288, K.289, G.290 Chain C: L.310, G.311 Ligands: MLI.1 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:I.41, A:A.259 Hydrogen bonds: A:G.260, A:R.261, A:E.282, A:D.283, A:D.283, A:W.286, A:G.288, A:K.289, A:G.290, C:L.310 Water bridges: A:H.42, A:N.284 Salt bridges: A:R.150, A:R.150, A:R.150 COA.5: 20 residues within 4Å: Chain B: I.41, H.42, F.142, M.147, R.150, Y.151, Y.197, L.226, L.257, A.259, G.260, R.261, E.282, D.283, W.286, A.287, G.288, K.289, G.290 Ligands: MLI.4 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.41, B:A.259 Hydrogen bonds: B:Y.151, B:G.260, B:R.261, B:E.282, B:D.283, B:D.283, B:W.286, B:G.288, B:G.290 Salt bridges: B:R.150, B:R.150, B:R.150

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.73, H.75, R.278, E.282 Ligands: MLI.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.73, A:H.75, A:E.282, H2O.7 ZN.6: 5 residues within 4Å: Chain B: H.73, H.75, R.278, E.282 Ligands: MLI.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.73, B:H.75, B:E.282, H2O.14 ZN.8: 5 residues within 4Å: Chain C: H.73, H.75, R.278, E.282 Ligands: MLI.7 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.73, C:H.75, C:E.282, H2O.22 ZN.10: 5 residues within 4Å: Chain D: H.73, H.75, R.278, E.282 Ligands: MLI.9 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.73, D:H.75, D:E.282, H2O.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Satanowski, A.G. et al., Design and implementation of aerobic, ambient CO2-reduction as an entry-point for enhanced carbon fixation. Nat Commun

Release Date

2025-01-01

Peptides

3-keto-5-aminohexanoate cleavage protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

3-keto-5-aminohexanoate cleavage protein