Research workbench
Crystal structure of biotin carboxylase from E.COLI in complex with potent inhibitor 3
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
- 2V5A
- Type
- protein
- Length
- 891 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.31
- Source
- ESCHERICHIA COLI
- Molecule
- Biotin carboxylase
- EC
- 6.3.4.14
- UniProt
- P24182
- Ligands
- LZL, CL
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.31 · 2 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Biotin carboxylase (EC 6.3.4.14) | protein | 446 | 37% helix, 26% strand | P24182 |
| B | Biotin carboxylase (EC 6.3.4.14) | protein | 445 | 36% helix, 25% strand | P24182 |
Ligands and binding sites
- LZL · 7-(2,5-dihydropyrrol-1-yl)-6-phenyl-pyrido[6,5-d]pyrimidin-2-amine · ligand · chains A
- 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
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 | 747 | 0.76 | 0.81 | 78 | LZL, CL |
| 2 | 343 | 0.76 | 0.87 | 50 | empty |
| 3 | 742 | 0.73 | 0.79 | 61 | CL |
| 4 | 74 | 0.39 | 0.78 | 12 | empty |
| 5 | 62 | 0.36 | 0.78 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1439 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 2V5A · Crystal structure of biotin carboxylase from E.COLI in complex with potent inhibitor 3 · 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 2V5A · PDBe 2V5A · UniProt P24182
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