Research workbench
Crystal structure of biotin carboxylase from E. COLI in complex with benzimidazole series
Analyse Crystal structure of biotin carboxylase from E. COLI in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JZI
- 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, 6.4.1.2
- UniProt
- P24182
- Ligands
- JZL
- Pockets
- 4 · best druggability 0.76
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, 6.4.1.2) | protein | 445 | 37% helix, 29% strand | P24182 |
| B | Biotin carboxylase (EC 6.3.4.14, 6.4.1.2) | protein | 446 | 36% helix, 27% strand | P24182 |
Ligands and binding sites
- JZL · 7-amino-2-[(2-chlorobenzyl)amino]-1-{[(1S,2S)-2-hydroxycycloheptyl]methyl}-1H-benzimidazole-5-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 796 | 0.76 | 0.80 | 75 | JZL |
| 2 | 333 | 0.75 | 0.86 | 52 | empty |
| 3 | 744 | 0.75 | 0.80 | 67 | JZL |
| 4 | 109 | 0.49 | 0.80 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1481 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3JZI · Crystal structure of biotin carboxylase from E. Coli in complex with benzimidazole series · 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 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 P24182
- Elsewhere: RCSB PDB 3JZI · PDBe 3JZI · UniProt P24182
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