Research workbench
Structure of the acetoacetyl-CoA THIOLASE/HMG-CoA synthase complex from methanothermococcus thermolithotrophicus soaked with acetyl-CoA
Analyse Structure of the acetoacetyl-CoA THIOLASE/HMG-CoA synthase complex from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ESQ
- Type
- protein
- Length
- 3,469 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetoacetyl-CoA thiolase; Pfam DUF35; Hydroxymethylglutaryl-CoA synthase
- EC
- 2.3.1.9, 2.3.3.10
- Ligands
- COA, K, ZN, NA, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Acetoacetyl-CoA thiolase (EC 2.3.1.9) | protein | 392 | 41% helix, 19% strand | — |
| E | Pfam DUF35 | protein | 127 | 11% helix, 46% strand | — |
| F | Pfam DUF35 | protein | 129 | 12% helix, 45% strand | — |
| G, H | Pfam DUF35 | protein | 128 | 15% helix, 42% strand | — |
| I, K, L | Hydroxymethylglutaryl-CoA synthase (EC 2.3.3.10) | protein | 347 | 42% helix, 27% strand | — |
| J | Hydroxymethylglutaryl-CoA synthase (EC 2.3.3.10) | protein | 348 | 43% helix, 25% strand | — |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, J, B, L, C, I, D, K
- K · Potassium ion · metal · 4 copies · chains B, I, K, J, L
- ZN · Zinc ion · metal · 4 copies · chains E, F, G, H
- NA · Sodium ion · metal · chains I, K
- CL · Chloride ion · ion · 3 copies · chains B, E, C, F, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.82 | 0.83 | 109 | COA |
| 2 | 972 | 0.79 | 0.81 | 79 | empty |
| 3 | 586 | 0.79 | 0.85 | 58 | empty |
| 4 | 490 | 0.78 | 0.86 | 53 | K |
| 5 | 599 | 0.78 | 0.84 | 69 | COA |
Interfaces
30 interfaces between chains.
- B–D · 2325 Ų buried · 47 hydrogen bonds · protein-protein
- J–L · 2322 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 2318 Ų buried · 56 hydrogen bonds · protein-protein
- I–K · 2285 Ų buried · 42 hydrogen bonds · protein-protein
- A–F · 1390 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6ESQ · Structure of the acetoacetyl-CoA thiolase/HMG-CoA synthase complex from… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6ESQ · PDBe 6ESQ
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