Research workbench
Crystal structure of vink-vinl covalent complex formed with a pantetheineamide cross-linking probe
Analyse Crystal structure of vink-vinl covalent complex formed with a pantetheineamide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F2R
- Type
- protein
- Length
- 764 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malonyl-CoA-[acyl-carrier-protein] transacylase; Acyl-carrier-protein
- UniProt
- Q76KY5, Q76KY4
- Ligands
- 9EF
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Malonyl-CoA-[acyl-carrier-protein] transacylase | protein | 303 | 50% helix, 18% strand | Q76KY5 |
| B, D | Acyl-carrier-protein | protein | 79 | 58% helix, 0% strand | Q76KY4 |
Ligands and binding sites
- 9EF · N-[2-(acetylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.82 | 0.84 | 78 | 9EF |
| 2 | 763 | 0.80 | 0.84 | 80 | 9EF |
| 3 | 311 | 0.57 | 0.77 | 45 | empty |
| 4 | 219 | 0.48 | 0.75 | 38 | empty |
| 5 | 74 | 0.43 | 0.81 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 678 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 678 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 507 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7F2R · Crystal structure of VinK-VinL covalent complex formed with a pantetheineamide… · 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 Q76KY5
- Every structure of UniProt Q76KY4
- Elsewhere: RCSB PDB 7F2R · PDBe 7F2R · UniProt Q76KY5 · UniProt Q76KY4
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