Research workbench
Structure of savm-W120K, streptavidin mutant
Analyse Structure of savm-W120K, streptavidin mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NQM
- Type
- protein
- Length
- 476 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- BTN
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 118 | 5% helix, 57% strand | P22629 |
| B, C | Streptavidin | protein | 119 | 5% helix, 56% strand | P22629 |
| D | Streptavidin | protein | 120 | 5% helix, 56% strand | P22629 |
Ligands and binding sites
- BTN · Biotin · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.76 | 0.81 | 91 | BTN |
| 2 | 519 | 0.74 | 0.82 | 73 | BTN |
| 3 | 177 | 0.54 | 0.80 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1541 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1523 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 476 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 459 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 216 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1NQM · Structure of Savm-W120K, streptavidin mutant · 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 1NQM · PDBe 1NQM · UniProt P22629
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