MolNFT v1 · #145304 · protein
Crystal structure of biotin acetyl coenzyme a carboxylase synthetase from helicobacter pylori with bound biotinylated ATP
6CK0: “Crystal structure of biotin acetyl coenzyme a carboxylase synthetase from helicobacter pylori with bound…”. X-ray diffraction, 2 ligands (F5D, SO4), 6 pockets (best druggability 0.78). MolNFT v1 #145304 on GenesisL1: 3D structure…
- PDB
- 6CK0
- Type
- protein
- Length
- 419 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biotin acetyl coenzyme a carboxylase synthetase
- UniProt
- B5Z8D8
- Ligands
- F5D, SO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Biotin acetyl coenzyme a carboxylase synthetase | protein | 209 | 30% helix, 34% strand | B5Z8D8 |
| B | Biotin acetyl coenzyme a carboxylase synthetase | protein | 210 | 30% helix, 35% strand | B5Z8D8 |
Ligands and binding sites
- F5D · 5'-O-[(S)-({5-[(2r,3as,4s,6ar)-2-hydroxyhexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}oxy){[(s)-hydroxy(phosphonooxy) phosphoryl]oxy}phosphoryl]adenosine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.78 | 0.80 | 85 | F5D |
| 2 | 235 | 0.63 | 0.82 | 37 | F5D |
| 3 | 108 | 0.48 | 0.80 | 21 | empty |
| 4 | 96 | 0.47 | 0.80 | 22 | empty |
| 5 | 71 | 0.35 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 682 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6CK0 · Crystal Structure of Biotin Acetyl Coenzyme A Carboxylase Synthetase from Helicobacter… · 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 B5Z8D8
- Elsewhere: RCSB PDB 6CK0 · PDBe 6CK0 · UniProt B5Z8D8
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