Research workbench
Crystal structure of acyl-CoA transferase from E. COLI O157:H7 (ydif)- thioester complex with CoA- 1
Analyse Crystal structure of acyl-CoA transferase from E. COLI O157:H7 (ydif)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AHV
- Type
- protein
- Length
- 2,048 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative enzyme ydif
- EC
- 2.8.3.-
- UniProt
- Q8X5X6
- Ligands
- COA
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative enzyme ydif (EC 2.8.3.-) | protein | 512 | 22% helix, 28% strand | Q8X5X6 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.81 | 0.97 | 36 | empty |
| 2 | 166 | 0.81 | 0.96 | 38 | empty |
| 3 | 555 | 0.80 | 0.86 | 79 | empty |
| 4 | 435 | 0.79 | 0.87 | 81 | empty |
| 5 | 254 | 0.73 | 0.87 | 54 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2677 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2610 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 804 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 796 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 14 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2AHV · Crystal Structure of Acyl-CoA transferase from E. coli O157:H7 (YdiF)-thioester complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8X5X6 · AlphaFold monomer V2.0 prediction for acetate CoA-transferase ydif (Q8X5X6) · 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 Q8X5X6
- Elsewhere: RCSB PDB 2AHV · PDBe 2AHV · UniProt Q8X5X6
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