Research workbench
Streptavidin mutant M88 (N49C/A86C)
Analyse Streptavidin mutant M88 (N49C/A86C) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VJK
- Type
- protein
- Length
- 1,452 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- BTN
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 8 distinct chains · 4% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 122 | 5% helix, 55% strand | P22629 |
| B | Streptavidin | protein | 118 | 5% helix, 57% strand | P22629 |
| C, K | Streptavidin | protein | 120 | 5% helix, 56% strand | P22629 |
| D, F, G, H | Streptavidin | protein | 123 | 2% helix, 54% strand | P22629 |
| E | Streptavidin | protein | 121 | 2% helix, 55% strand | P22629 |
| I | Streptavidin | protein | 121 | 5% helix, 55% strand | P22629 |
| J | Streptavidin | protein | 119 | 3% helix, 56% strand | P22629 |
| L | Streptavidin | protein | 119 | 3% helix, 55% strand | P22629 |
Ligands and binding sites
- BTN · Biotin · ligand · 12 copies · chains A, B, C, I, D, J, E, F, G, H, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 981 | 0.79 | 0.81 | 106 | empty |
| 2 | 693 | 0.72 | 0.78 | 75 | BTN |
| 3 | 784 | 0.67 | 0.75 | 68 | empty |
| 4 | 376 | 0.66 | 0.80 | 58 | empty |
| 5 | 125 | 0.60 | 0.84 | 25 | BTN |
Interfaces
27 interfaces between chains.
- C–D · 1639 Ų buried · 31 hydrogen bonds · protein-protein
- K–L · 1632 Ų buried · 31 hydrogen bonds · protein-protein
- G–H · 1629 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1626 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 1623 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6VJK · Streptavidin mutant M88 (N49C/A86C) · 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 6VJK · PDBe 6VJK · UniProt P22629
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