Research workbench
Cis-divalent streptavidin
Analyse Cis-divalent streptavidin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BX5
- Type
- protein
- Length
- 480 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 120 | 8% helix, 56% strand | P22629 |
| B | Streptavidin | protein | 121 | 2% helix, 56% strand | P22629 |
| C | Streptavidin | protein | 119 | 8% helix, 57% strand | P22629 |
| D | Streptavidin | protein | 120 | 5% helix, 57% strand | P22629 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C
- PG4 · Tetraethylene glycol · additive · 2 copies · chains B, D
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 | 629 | 0.70 | 0.78 | 69 | EDO |
| 2 | 559 | 0.69 | 0.79 | 61 | EDO |
| 3 | 138 | 0.59 | 0.83 | 25 | PG4 |
| 4 | 120 | 0.57 | 0.84 | 25 | PG4 |
Interfaces
6 interfaces between chains.
- C–D · 1640 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1574 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 543 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 394 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 215 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4BX5 · cis-divalent streptavidin · 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 4BX5 · PDBe 4BX5 · UniProt P22629
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