SMTL ID : 6esq.1

Structure of the acetoacetyl-CoA thiolase/HMG-CoA synthase complex from Methanothermococcus thermolithotrophicus soaked with acetyl-CoA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

hetero-4-4-4-mer

Ligands

4 x COA: COENZYME A(Non-covalent)

COA.1: 12 residues within 4Å: Chain A: F.182, F.184, S.195, V.197, L.203, M.204, C.206, S.207, P.208, K.332 Chain J: R.203, K.243 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain J Hydrogen bonds: A:C.206, A:K.332 Salt bridges: J:R.203, J:R.203, J:K.243, J:K.243 COA.2: 14 residues within 4Å: Chain B: P.142, H.171, F.182, F.184, V.197, L.203, M.204, C.206, S.207, P.208, V.209, K.332 Chain L: R.203, K.243 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain L Hydrogen bonds: B:C.206, B:S.207, B:K.332 pi-Stacking: B:F.182 Salt bridges: L:R.203, L:K.243 COA.5: 13 residues within 4Å: Chain C: H.171, F.182, F.184, V.197, L.203, M.204, C.206, S.207, P.208, V.209, K.332 Chain I: R.203, K.243 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain I Hydrogen bonds: C:C.206, C:V.209, C:K.332, I:R.203 pi-Stacking: C:F.182 Salt bridges: I:R.203, I:K.243 COA.6: 16 residues within 4Å: Chain D: T.122, P.142, H.171, F.182, F.184, V.197, L.203, M.204, C.206, S.207, P.208, V.209, F.287, K.332 Chain K: R.203, K.243 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain K Hydrophobic interactions: D:L.203 Hydrogen bonds: D:C.206, D:K.332 Salt bridges: K:R.203, K:K.243

4 x K: POTASSIUM ION(Non-covalent)

K.3: 3 residues within 4Å: Chain B: D.36, K.354, D.356 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.36 K.4: 2 residues within 4Å: Chain B: D.3, R.392 No protein-ligand interaction detected (PLIP) K.14: 3 residues within 4Å: Chain I: A.87, E.111 Chain K: E.111 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain K Metal complexes: I:E.111, K:E.111 K.16: 4 residues within 4Å: Chain J: A.87, E.111 Chain L: E.111, E.193 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain L Metal complexes: J:E.111, L:E.111

4 x ZN: ZINC ION(Non-covalent)

ZN.7: 6 residues within 4Å: Chain E: C.20, C.23, Y.27, C.34, D.36, C.37 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.20, E:C.23, E:C.34, E:C.37 ZN.9: 6 residues within 4Å: Chain F: C.20, C.23, Y.27, C.34, D.36, C.37 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.23, F:C.34, F:C.37 ZN.11: 7 residues within 4Å: Chain G: C.20, T.22, C.23, Y.27, C.34, D.36, C.37 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:C.20, G:C.34 ZN.13: 6 residues within 4Å: Chain H: C.20, C.23, Y.27, C.34, D.36, C.37 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.20, H:C.23, H:C.34, H:C.37

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

CL.8: 3 residues within 4Å: Chain B: G.41 Chain E: R.38, R.39 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain C: D.40, G.41 Chain F: R.38, R.39 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain D: G.41 Chain G: R.38, R.39 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.15: 7 residues within 4Å: Chain I: V.88, K.89, P.90, D.109 Chain K: E.111, F.112, A.113 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:E.111, K:A.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vogeli, B. et al., Archaeal acetoacetyl-CoA thiolase/HMG-CoA synthase complex channels the intermediate via a fused CoA-binding site. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-03-14

Peptides

acetoacetyl-CoA thiolase: ABCD
Pfam DUF35: EFGH
HydroxyMethylGlutaryl-CoA synthase: IJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

acetoacetyl-CoA thiolase

Pfam DUF35

HydroxyMethylGlutaryl-CoA synthase

Related Entries With Identical Sequence