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Biosynthetic thiolase from Z. ramigera. complex of with O-pantheteine- 11-pivalate.
Analyse Biosynthetic thiolase from Z. ramigera. complex of with O-pantheteine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VU1
- Type
- protein
- Length
- 1,564 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl-CoA acetyltransferase
- EC
- 2.3.1.9
- UniProt
- P07097
- Ligands
- OPI, NA, SO4
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 391 | 39% helix, 23% strand | P07097 |
| B | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 392 | 39% helix, 23% strand | P07097 |
| D | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 390 | 38% helix, 23% strand | P07097 |
Ligands and binding sites
- OPI · Pantothenyl-aminoethanol-11-pivalic acid · ligand · 2 copies · chains A, D, B, C
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.79 | 0.99 | 35 | empty |
| 2 | 103 | 0.78 | 0.98 | 34 | empty |
| 3 | 223 | 0.64 | 0.82 | 30 | OPI |
| 4 | 193 | 0.60 | 0.82 | 27 | empty |
| 5 | 182 | 0.60 | 0.81 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2628 Ų buried · 76 hydrogen bonds · protein-protein
- C–D · 2608 Ų buried · 74 hydrogen bonds · protein-protein
- B–C · 681 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 667 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 311 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 2VU1 · Biosynthetic thiolase from Z. ramigera. Complex of with O-pantheteine- 11-pivalate. · the same entry in another collection · chain A against A, TM-score 1.00
- P07097 · AlphaFold monomer V2.0 prediction for acetyl-CoA acetyltransferase (P07097) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P07097
- Elsewhere: RCSB PDB 2VU1 · PDBe 2VU1 · UniProt P07097
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