Research workbench
Crystal structure of biotin carboxylase from E.COLI in complex with potent inhibitor 1
Analyse Crystal structure of biotin carboxylase from E.COLI in complex with potent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V58
- Type
- protein
- Length
- 891 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biotin carboxylase
- EC
- 6.3.4.14
- UniProt
- P24182
- Ligands
- LZJ, CL
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Biotin carboxylase (EC 6.3.4.14) | protein | 446 | 37% helix, 28% strand | P24182 |
| B | Biotin carboxylase (EC 6.3.4.14) | protein | 445 | 36% helix, 27% strand | P24182 |
Ligands and binding sites
- LZJ · 6-(2,6-dibromophenyl)pyrido[2,3-d]pyrimidine-2,7-diamine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 730 | 0.75 | 0.80 | 76 | LZJ, CL |
| 2 | 324 | 0.74 | 0.86 | 49 | empty |
| 3 | 703 | 0.73 | 0.79 | 61 | LZJ, CL |
| 4 | 63 | 0.37 | 0.78 | 12 | empty |
| 5 | 60 | 0.35 | 0.77 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1443 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 2V58 · Crystal structure of biotin carboxylase from E.COLI in complex with potent inhibitor 1 · the same entry in another collection · chain A against A, TM-score 1.00
- P24182 · AlphaFold monomer V2.0 prediction for biotin carboxylase (P24182) · a predicted model of the same protein · chain B 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 P24182
- Elsewhere: RCSB PDB 2V58 · PDBe 2V58 · UniProt P24182
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