Research workbench
Streptavidin mutant Y43F with biotin at 1.81A resolution
Analyse Streptavidin mutant Y43F with biotin at 1.81A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NDJ
- Type
- protein
- Length
- 468 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- BTN
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Streptavidin | protein | 117 | 5% helix, 58% strand | P22629 |
Ligands and binding sites
- BTN · Biotin · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.68 | 0.83 | 48 | BTN |
| 2 | 246 | 0.68 | 0.84 | 51 | BTN |
| 3 | 320 | 0.65 | 0.81 | 44 | empty |
| 4 | 330 | 0.64 | 0.80 | 49 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1634 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1619 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 544 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 537 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 207 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1NDJ · Streptavidin Mutant Y43F with Biotin at 1.81A Resolution · 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 P22629
- Elsewhere: RCSB PDB 1NDJ · PDBe 1NDJ · UniProt P22629
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