Research workbench
Structure of the acetoacetyl-CoA-THIOLASE/HMG-CoA-synthase complex from methanothermococcus thermolithotrophicus at 2.75 a
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
- 6ET9
- Type
- protein
- Length
- 3,466 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl-CoA acetyltransferase thiolase; Pfam DUF35; Hydroxymethylglutaryl-CoA synthase
- EC
- 2.3.1.9, 2.3.3.10
- Ligands
- K, ZN, NA, MG, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Acetyl-CoA acetyltransferase thiolase (EC 2.3.1.9) | protein | 392 | 42% helix, 20% strand | — |
| C | Acetyl-CoA acetyltransferase thiolase (EC 2.3.1.9) | protein | 389 | 42% helix, 19% strand | — |
| E, F, G, H | Pfam DUF35 | protein | 128 | 15% helix, 45% strand | — |
| I, K, L | Hydroxymethylglutaryl-CoA synthase (EC 2.3.3.10) | protein | 347 | 43% helix, 27% strand | — |
| J | Hydroxymethylglutaryl-CoA synthase (EC 2.3.3.10) | protein | 348 | 43% helix, 25% strand | — |
Ligands and binding sites
- K · Potassium ion · metal · 8 copies · chains A, B, C, D, I, K, J, L
- ZN · Zinc ion · metal · 4 copies · chains E, F, G, H
- NA · Sodium ion · metal · 3 copies · chains A, D, J
- MG · Magnesium ion · metal · chains D
- CL · Chloride ion · ion · 6 copies · chains C, F, E, L, B, D, G, A, H, I, K
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 11 copies · chains A, L, B, D, C, I, F, G, K, H, J
- GOL · Glycerol · additive · 6 copies · chains I, J, K, L
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 | 832 | 0.85 | 0.87 | 99 | K |
| 2 | 948 | 0.81 | 0.82 | 89 | empty |
| 3 | 726 | 0.80 | 0.84 | 76 | empty |
| 4 | 442 | 0.80 | 0.88 | 51 | empty |
| 5 | 829 | 0.79 | 0.82 | 87 | empty |
Interfaces
30 interfaces between chains.
- B–D · 2347 Ų buried · 51 hydrogen bonds · protein-protein
- A–C · 2346 Ų buried · 55 hydrogen bonds · protein-protein
- I–K · 2266 Ų buried · 41 hydrogen bonds · protein-protein
- J–L · 2234 Ų buried · 39 hydrogen bonds · protein-protein
- A–F · 1389 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6ET9 · 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 6ET9 · PDBe 6ET9
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