MolNFT v1 · #88266 · protein
Streptavidin A86D mutant with love-hate ligand 4
4CPI: “Streptavidin A86D mutant with love-hate ligand 4”. X-ray diffraction, 2 ligands (LH4, CA), 5 pockets (best druggability 0.46). MolNFT v1 #88266 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4CPI
- Type
- protein
- Length
- 474 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- LH4, CA
- Pockets
- 5 · best druggability 0.46
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 119 | 8% helix, 56% strand | P22629 |
| B | Streptavidin | protein | 118 | 8% helix, 58% strand | P22629 |
| C | Streptavidin | protein | 117 | 8% helix, 57% strand | P22629 |
| D | Streptavidin | protein | 120 | 8% helix, 56% strand | P22629 |
Ligands and binding sites
- LH4 · 5-[(3aS,4S,6aR)-2-oxo-hexahydro-1H-thieno[3,4- d]imidazolidin-4-yl]-N'-{2,6-bis[4-(morpholine-4- sulfonyl)phenyl]phenyl}pentanehydrazide · ligand · 4 copies · chains A, C, B, D
- CA · Calcium ion · metal · 2 copies · chains A, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.46 | 0.75 | 36 | empty |
| 2 | 159 | 0.45 | 0.75 | 19 | LH4 |
| 3 | 139 | 0.42 | 0.75 | 24 | empty |
| 4 | 94 | 0.38 | 0.75 | 16 | empty |
| 5 | 67 | 0.31 | 0.74 | 14 | LH4 |
Interfaces
3 interfaces between chains.
- A–B · 1605 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 431 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 27 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4CPI · streptavidin A86D mutant with love-hate ligand 4 · 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 4CPI · PDBe 4CPI · UniProt P22629
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