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Crystal structure analysis of thiolase-like protein, ST0096 from sulfolobus tokodaii
Analyse Crystal structure analysis of thiolase-like protein, ST0096 from sulfolobus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YZO
- Type
- protein
- Length
- 1,411 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative acyl-CoA acyltransferase
- EC
- 2.3.1.-
- UniProt
- Q976U3
- Ligands
- CA
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative acyl-CoA acyltransferase (EC 2.3.1.-) | protein | 363 | 38% helix, 22% strand | Q976U3 |
| B | Putative acyl-CoA acyltransferase (EC 2.3.1.-) | protein | 354 | 38% helix, 23% strand | Q976U3 |
| C, D | Putative acyl-CoA acyltransferase (EC 2.3.1.-) | protein | 347 | 40% helix, 21% strand | Q976U3 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains C, D
- PEG · Di(hydroxyethyl)ether · additive · 8 copies · chains A, B, C, D
- IMD · Imidazole · additive · chains A
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.73 | 0.80 | 72 | empty |
| 2 | 521 | 0.70 | 0.79 | 69 | PEG |
| 3 | 93 | 0.69 | 0.93 | 30 | empty |
| 4 | 53 | 0.65 | 0.95 | 20 | empty |
| 5 | 84 | 0.52 | 0.84 | 22 | PEG |
Interfaces
5 interfaces between chains.
- A–C · 1978 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 1819 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 354 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 286 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 60 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4YZO · Crystal Structure Analysis of Thiolase-like protein, ST0096 from Sulfolobus Tokodaii · 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
- Every structure of UniProt Q976U3
- Elsewhere: RCSB PDB 4YZO · PDBe 4YZO · UniProt Q976U3
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