MolNFT v1 · #77970 · protein
Crystal structure of E.COLI biotin carboxylase in complex with two ADP and two ca ions
3RUP: “Crystal structure of E.COLI biotin carboxylase in complex with two ADP and two ca ions”. X-ray diffraction, 3 ligands (ADP, CA, CL), 3 pockets (best druggability 0.81). MolNFT v1 #77970 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3RUP
- Type
- protein
- Length
- 890 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
- ADP, CA, CL
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Biotin carboxylase (EC 6.3.4.14, 6.4.1.2) | protein | 444 | 36% helix, 27% 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
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.81 | 0.83 | 86 | ADP, CA |
| 2 | 839 | 0.80 | 0.83 | 78 | ADP, CA, CL |
| 3 | 581 | 0.74 | 0.82 | 59 | empty |
Interfaces
1 interface between chains.
- A–B · 1305 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3RUP · Crystal structure of E.coli biotin carboxylase in complex with two ADP and two Ca ions · 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 0.95
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 3RUP · PDBe 3RUP · UniProt P24182
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