MolNFT v1 · #52984 · protein
Crystal structure of human acyl-CoA binding domain 4 complexed with stearoyl-CoA
2WH5 · Acyl-CoA-binding domain-containing protein 4: “Crystal structure of human acyl-CoA binding domain 4 complexed with stearoyl-CoA”. X-ray diffraction, 3 ligands (STE, ST9, COA), 11 pockets (best druggability 0.61). MolNFT v1 #52984 on…
- PDB
- 2WH5
- Type
- protein
- Length
- 536 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA-binding domain-containing protein 4
- UniProt
- Q8NC06
- Ligands
- STE, ST9, COA
- Pockets
- 11 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Acyl-CoA-binding domain-containing protein 4 | protein | 90 | 66% helix, 0% strand | Q8NC06 |
| B, D, E, F | Acyl-CoA-binding domain-containing protein 4 | protein | 89 | 64% helix, 1% strand | Q8NC06 |
Ligands and binding sites
- STE · Stearic acid · ligand · 6 copies · chains A, B, C, D, E, F
- ST9 · Stearoyl-coenzyme A · ligand · 6 copies · chains A, B, C, D, E, F
- COA · Coenzyme A · ligand · 2 copies · chains B, C, D, F, A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.61 | 0.77 | 43 | COA |
| 2 | 344 | 0.60 | 0.77 | 40 | COA |
| 3 | 141 | 0.47 | 0.77 | 21 | STE |
| 4 | 178 | 0.47 | 0.75 | 18 | STE |
| 5 | 183 | 0.46 | 0.74 | 22 | STE |
Interfaces
10 interfaces between chains.
- B–C · 291 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 274 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 246 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 241 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 229 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2WH5 · Crystal structure of human acyl-CoA binding domain 4 complexed with stearoyl-CoA · the same entry in another collection · chain F against F, TM-score 1.00
- Q8NC06 · AlphaFold monomer V2.0 prediction for acyl-CoA-binding domain- containing protein 4… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8NC06
- Elsewhere: RCSB PDB 2WH5 · PDBe 2WH5 · UniProt Q8NC06
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