MolNFT v1 · #22138 · protein
Apo-core-streptavidin in complex with biotin (two unoccupied binding sites) at pH 4.5
1SWD: “Apo-core-streptavidin in complex with biotin (two unoccupied binding sites) at pH 4.5”. X-ray diffraction, 1 ligand (BTN), 7 pockets (best druggability 0.60). MolNFT v1 #22138 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1SWD
- Type
- protein
- Length
- 464 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- BTN
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 117 | 3% helix, 57% strand | P22629 |
| B | Streptavidin | protein | 114 | 8% helix, 57% strand | P22629 |
| C | Streptavidin | protein | 115 | 8% helix, 58% strand | P22629 |
| D | Streptavidin | protein | 118 | 5% helix, 58% strand | P22629 |
Ligands and binding sites
- BTN · Biotin · ligand · 2 copies · chains A, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.60 | 0.77 | 41 | empty |
| 2 | 130 | 0.58 | 0.83 | 27 | BTN |
| 3 | 110 | 0.58 | 0.85 | 25 | BTN |
| 4 | 179 | 0.56 | 0.80 | 22 | empty |
| 5 | 159 | 0.56 | 0.82 | 27 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1660 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1581 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 544 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 406 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 201 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1SWD · Apo-core-streptavidin in complex with biotin (two unoccupied binding sites) at pH 4.5 · 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 1SWD · PDBe 1SWD · UniProt P22629
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