Research workbench
Crystal structure of rhizavidin-biotin complex
Analyse Crystal structure of rhizavidin-biotin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EW2
- Type
- protein
- Length
- 802 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhizavidin
- UniProt
- Q8KKW2
- Ligands
- BTN
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 0% helix, 65% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhizavidin | protein | 114 | 0% helix, 68% strand | Q8KKW2 |
| B | Rhizavidin | protein | 121 | 0% helix, 67% strand | Q8KKW2 |
| C | Rhizavidin | protein | 124 | 3% helix, 65% strand | Q8KKW2 |
| D | Rhizavidin | protein | 95 | 0% helix, 54% strand | Q8KKW2 |
| E | Rhizavidin | protein | 119 | 0% helix, 67% strand | Q8KKW2 |
| F | Rhizavidin | protein | 119 | 0% helix, 64% strand | Q8KKW2 |
| G | Rhizavidin | protein | 110 | 0% helix, 69% strand | Q8KKW2 |
Ligands and binding sites
- BTN · Biotin · ligand · 7 copies · chains A, B, F, C, D, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.83 | 0.85 | 105 | BTN |
| 2 | 318 | 0.75 | 0.87 | 59 | empty |
| 3 | 86 | 0.72 | 0.95 | 22 | BTN |
| 4 | 228 | 0.68 | 0.85 | 39 | empty |
| 5 | 67 | 0.55 | 0.87 | 19 | empty |
Interfaces
14 interfaces between chains.
- F–G · 1389 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1385 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1374 Ų buried · 19 hydrogen bonds · protein-protein
- B–F · 1262 Ų buried · 28 hydrogen bonds · protein-protein
- C–E · 809 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 3EW2 · Crystal structure of rhizavidin-biotin complex · 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 Q8KKW2
- Elsewhere: RCSB PDB 3EW2 · PDBe 3EW2 · UniProt Q8KKW2
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