MolNFT v1 · #77400 · protein
Crystal structure of ligand-free R7-2 streptavidin
3RDX: “Crystal structure of ligand-free R7-2 streptavidin”. X-ray diffraction, 2 pockets (best druggability 0.62). MolNFT v1 #77400 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3RDX
- Type
- protein
- Length
- 249 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 124 | 7% helix, 54% strand | P22629 |
| B | Streptavidin | protein | 125 | 9% helix, 54% strand | P22629 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.62 | 0.85 | 29 | GOL |
| 2 | 171 | 0.61 | 0.83 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 501 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3RDX · Crystal structure of ligand-free R7-2 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 3RDX · PDBe 3RDX · UniProt P22629
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