Research workbench
Crystal structure at 2.1 a of the S-component for biotin from an ecf- type ABC transporter
Analyse Crystal structure at 2.1 a of the S-component for biotin from an ecf- type ABC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DVE
- Type
- protein
- Length
- 566 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biotin transporter bioy
- UniProt
- A2RMJ9
- Ligands
- BNG, BTN
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Biotin transporter bioy | protein | 189 | 74% helix, 2% strand | A2RMJ9 |
| C | Biotin transporter bioy | protein | 188 | 73% helix, 2% strand | A2RMJ9 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 6 copies · chains A, C, B
- BTN · Biotin · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 559 | 0.73 | 0.80 | 60 | BNG |
| 2 | 187 | 0.63 | 0.83 | 30 | BTN |
| 3 | 124 | 0.63 | 0.87 | 20 | BTN |
| 4 | 312 | 0.62 | 0.78 | 29 | empty |
| 5 | 144 | 0.62 | 0.85 | 29 | BTN |
Interfaces
2 interfaces between chains.
- B–C · 862 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 544 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 4DVE · Crystal structure at 2.1 A of the S-component for biotin from an ECF-type ABC transporter · the same entry in another collection · chain A against A, TM-score 1.00
- A2RMJ9 · AlphaFold monomer V2.0 prediction for biotin transporter bioy (A2RMJ9) · a predicted model of the same protein · chain C 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 A2RMJ9
- Elsewhere: RCSB PDB 4DVE · PDBe 4DVE · UniProt A2RMJ9
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