Research workbench
Crystal structure of biotin carboxylase from S. aureus complexed with amppnp
Analyse Crystal structure of biotin carboxylase from S. aureus complexed with amppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VPQ
- Type
- protein
- Length
- 895 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl-CoA carboxylase
- EC
- 6.3.4.14
- UniProt
- Q99TW7
- Ligands
- ANP, MG, CL
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetyl-CoA carboxylase (EC 6.3.4.14) | protein | 447 | 35% helix, 27% strand | Q99TW7 |
| B | Acetyl-CoA carboxylase (EC 6.3.4.14) | protein | 448 | 37% helix, 27% strand | Q99TW7 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.79 | 0.81 | 85 | ANP, MG, CL |
| 2 | 966 | 0.78 | 0.80 | 83 | ANP, MG, CL |
| 3 | 409 | 0.74 | 0.84 | 41 | empty |
| 4 | 133 | 0.69 | 0.90 | 38 | empty |
| 5 | 68 | 0.34 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1363 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2VPQ · Crystal structure of biotin carboxylase from S. aureus complexed with AMPPNP · 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 Q99TW7
- Elsewhere: RCSB PDB 2VPQ · PDBe 2VPQ · UniProt Q99TW7
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