SMTL ID : 6pcc.1

Crystal structure of beta-ketoadipyl-CoA thiolase mutant (H356A) in complex hexanoyl coenzyme A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-tetramer

Ligands

4 x COA: COENZYME A(Non-covalent)

COA.1: 19 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, C.409 9 PLIP interactions: 9 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 pi-Cation interactions: A:R.249, A:R.249 COA.4: 17 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, F.348, A.379, L.381 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.168, B:A.275 Hydrogen bonds: 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: 17 residues within 4Å: Chain C: C.113, I.168, M.186, P.187, R.249, T.252, L.260, A.272, G.273, A.275, S.276, G.277, N.345, A.347, F.348, A.379, L.381 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.168, C:P.187, C:A.275 Hydrogen bonds: C:Q.212, C:R.249, C:R.249, C:T.252, C:S.276 Water bridges: 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, D:G.277 pi-Cation interactions: D:R.249

4 x O8Y: hexanal(Non-covalent)

O8Y.2: 10 residues within 4Å: Chain A: N.81, L.112, T.166, T.167, I.168, G.169, R.171, M.186, L.381 Chain D: R.88 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:N.81, A:I.168, A:L.381, D:R.88 Water bridges: A:G.411 Hydrogen bonds: D:R.88 O8Y.5: 9 residues within 4Å: Chain B: N.81, L.112, T.166, I.168, G.169, R.171, M.186, L.381 Chain C: R.88 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:R.88, B:N.81, B:I.168 Water bridges: B:C.113 O8Y.8: 11 residues within 4Å: Chain B: R.88 Chain C: A.80, N.81, L.112, T.166, T.167, I.168, G.169, R.171, M.186, L.381 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:A.80, C:N.81, C:I.168, C:L.381 Water bridges: C:C.113 Hydrogen bonds: B:R.88 O8Y.11: 10 residues within 4Å: Chain A: R.88 Chain D: N.81, L.112, T.166, T.167, I.168, G.169, R.171, M.186, L.381 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:N.81, D:I.168, D:L.381, A:R.88 Water bridges: D:C.113 Hydrogen bonds: A:R.88

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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.6: 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 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.210, B:E.346, B:D.363, B:N.369, B:N.369 Water bridges: B:K.214 GOL.9: 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 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.210, C:K.214, C:E.346, C:D.363, C:N.369 Water bridges: C:K.214 GOL.12: 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

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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