MolNFT v1 · #177496 · protein
Crystal structure of apo streptavidin at cryogenic temperature
7EK9: “Crystal structure of apo streptavidin at cryogenic temperature”. X-ray diffraction, 4 pockets (best druggability 0.68). MolNFT v1 #177496 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7EK9
- Type
- protein
- Length
- 482 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 121 | 5% helix, 55% strand | P22629 |
| B | Streptavidin | protein | 121 | 7% helix, 55% strand | P22629 |
| C, D | Streptavidin | protein | 120 | 5% helix, 56% strand | P22629 |
Ligands and binding sites
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 3 copies · chains A, D, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 574 | 0.68 | 0.78 | 68 | MRD, MPD |
| 2 | 539 | 0.68 | 0.78 | 55 | MRD |
| 3 | 155 | 0.62 | 0.84 | 29 | MRD |
| 4 | 190 | 0.50 | 0.76 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1612 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1533 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 472 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 404 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 203 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7EK9 · Crystal structure of apo streptavidin at cryogenic temperature · 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 7EK9 · PDBe 7EK9 · UniProt P22629
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