SMTL ID : 9jhz.1

3-Hydroxybutyryl-CoA dehydrogenase mutant(S117A) with acetoacetyl CoA and NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

2 x CAA: ACETOACETYL-COENZYME A(Non-covalent)

CAA.1: 20 residues within 4Å: Chain C: L.52, K.55, K.57, I.58, A.118, H.137, F.139, N.140, R.144, N.187, L.190, P.222, M.223, L.228, I.232, I.240 Chain F: G.218, A.219, N.220 Ligands: NAD.2 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:F.139, C:I.232, C:I.240 Hydrogen bonds: C:N.140, C:N.140, C:N.187, F:N.220 Salt bridges: C:K.55, C:K.57, C:R.144 pi-Cation interactions: C:R.144, C:R.144 CAA.3: 20 residues within 4Å: Chain C: G.218, A.219, N.220 Chain F: L.52, K.55, K.57, I.58, A.118, H.137, F.139, N.140, R.144, N.187, L.190, P.222, M.223, L.228, I.232, I.240 Ligands: NAD.4 12 PLIP interactions: 11 interactions with chain F, 1 interactions with chain C Hydrophobic interactions: F:F.139, F:I.232, F:I.240 Hydrogen bonds: F:N.140, F:N.140, F:N.187, C:N.220 Salt bridges: F:K.55, F:K.57, F:R.144 pi-Cation interactions: F:R.144, F:R.144

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 23 residues within 4Å: Chain C: G.8, G.10, T.11, M.12, D.32, I.33, A.88, A.89, F.90, E.91, V.95, K.96, T.99, N.116, A.118, H.137, F.138, N.140, I.232, D.235, I.236, K.271 Ligands: CAA.1 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:T.11, C:T.11, C:T.11, C:M.12, C:I.33, C:A.89, C:F.90, C:K.96, C:T.99, C:N.116, C:A.118, C:N.140, C:I.232 Water bridges: C:G.10, C:G.10 Salt bridges: C:K.271 NAD.4: 23 residues within 4Å: Chain F: G.8, G.10, T.11, M.12, D.32, I.33, A.88, A.89, F.90, E.91, V.95, K.96, T.99, N.116, A.118, H.137, F.138, N.140, I.232, D.235, I.236, K.271 Ligands: CAA.3 19 PLIP interactions: 19 interactions with chain F Hydrogen bonds: F:T.11, F:T.11, F:T.11, F:M.12, F:D.32, F:I.33, F:A.89, F:F.90, F:E.91, F:K.96, F:T.99, F:T.99, F:N.116, F:A.118, F:N.140, F:I.232 Water bridges: F:G.10, F:G.10 Salt bridges: F:K.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, J. et al., Structural Insights and Catalytic Mechanism of 3-Hydroxybutyryl-CoA Dehydrogenase from Faecalibacterium Prausnitzii A2-165. Int J Mol Sci (2024)

Release Date

2024-11-13

Peptides

3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

D
C

E
A

F
B

3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein