SMTL ID : 6pcb.1

Crystal structure of beta-ketoadipyl-CoA thiolase mutant (H356A) in complex with COA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-tetramer

Ligands

4 x COA: COENZYME A(Non-covalent)

COA.1: 18 residues within 4Å: Chain A: C.113, I.168, M.186, R.249, T.252, L.257, L.260, A.272, G.273, A.275, S.276, G.277, V.278, N.345, A.347, F.348, A.379, L.381 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.168, A:A.275 Hydrogen bonds: A:T.252, A:S.276, A:S.276, A:V.278 Water bridges: A:Q.212, A:R.249, A:R.249 Salt bridges: A:R.249 COA.4: 18 residues within 4Å: Chain B: C.113, I.168, M.186, R.249, T.252, L.257, L.260, A.272, G.273, A.275, S.276, G.277, V.278, N.345, A.347, F.348, A.379, L.381 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.168, B:A.275 Hydrogen bonds: B:R.249, B:T.252, B:S.276, B:S.276, B:V.278 Water bridges: B:R.249, B:R.249 Salt bridges: B:R.249 COA.7: 18 residues within 4Å: Chain C: C.113, I.168, M.186, P.187, R.249, T.252, L.257, L.260, A.272, G.273, A.275, S.276, G.277, N.345, F.348, A.379, L.381 Ligands: CL.9 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.168, C:P.187, C:A.275 Hydrogen bonds: C:R.249, C:R.249, C:T.252, C:S.276 Water bridges: C:Q.212, C:V.278 pi-Cation interactions: C:R.249 COA.10: 17 residues within 4Å: Chain D: C.113, I.168, M.186, R.249, T.252, L.257, L.260, A.272, G.273, A.275, S.276, G.277, V.278, N.345, F.348, A.379, L.381 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:I.168, D:A.275 Hydrogen bonds: D:R.249, D:T.252, D:S.276, D:S.276, D:V.278 Water bridges: D:Q.212, D:R.249, D:R.249 Salt bridges: D:R.249 pi-Cation interactions: D:R.249

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 residues within 4Å: Chain A: F.207, R.210, S.211, K.214, E.346, D.363, D.364, V.368, N.369, G.372, G.373 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.210, A:K.214, A:E.346, A:D.363 Water bridges: A:K.214 GOL.5: 11 residues within 4Å: Chain B: F.207, R.210, S.211, K.214, E.346, D.363, D.364, V.368, N.369, G.372, G.373 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.210, B:E.346, B:D.363, B:N.369 Water bridges: B:K.214 GOL.8: 11 residues within 4Å: Chain C: F.207, R.210, S.211, K.214, E.346, D.363, D.364, V.368, N.369, G.372, G.373 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.210, C:K.214, C:E.346, C:D.363 Water bridges: C:K.214 GOL.11: 11 residues within 4Å: Chain D: F.207, R.210, S.211, K.214, E.346, D.363, D.364, V.368, N.369, G.372, G.373 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.210, D:E.346, D:D.363, D:N.369 Water bridges: D:K.214

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 5 residues within 4Å: Chain A: N.345, A.374, S.384, R.387, L.388 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain B: R.88 Chain C: I.168, G.169, R.171, L.381 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain C: M.143, G.277, V.278, A.379, L.381 Ligands: COA.7 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain D: G.169, S.185, M.186, P.187 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain A: I.168, G.169, R.171, L.381 Chain D: R.88 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhaskar, S. et al., Structural basis for differentiation between two classes of thiolase: Degradative vs biosynthetic thiolase. J Struct Biol X (2020)

Release Date

2020-05-27

Peptides

Beta-ketoadipyl-CoA thiolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Beta-ketoadipyl-CoA thiolase

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