Research workbench
Circular permuted streptavidin N49/G48
Analyse Circular permuted streptavidin N49/G48 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GD9
- Type
- protein
- Length
- 496 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- BTN, SO4
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 120 | 8% helix, 57% strand | P22629 |
| B | Streptavidin | protein | 131 | 11% helix, 54% strand | P22629 |
| C | Streptavidin | protein | 123 | 11% helix, 57% strand | P22629 |
| D | Streptavidin | protein | 122 | 11% helix, 56% strand | P22629 |
Ligands and binding sites
- BTN · Biotin · ligand · 4 copies · chains A, D, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.65 | 0.79 | 54 | empty |
| 2 | 206 | 0.57 | 0.80 | 32 | empty |
| 3 | 147 | 0.56 | 0.82 | 28 | BTN |
| 4 | 93 | 0.56 | 0.85 | 20 | BTN |
| 5 | 166 | 0.56 | 0.80 | 29 | BTN |
Interfaces
6 interfaces between chains.
- C–D · 1625 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1585 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 573 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 545 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 211 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4GD9 · Circular Permuted Streptavidin N49/G48 · 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 4GD9 · PDBe 4GD9 · UniProt P22629
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.