MolNFT v1 · #115731 · protein
Streptavidin-S112Y-K121E complexed with palladium-containing biotin ligand
5CSE: “Streptavidin-S112Y-K121E complexed with palladium-containing biotin ligand”. X-ray diffraction, 2 ligands (SVP, CL), 3 pockets (best druggability 0.48). MolNFT v1 #115731 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5CSE
- Type
- protein
- Length
- 243 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- SVP, CL
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 121 | 6% helix, 55% strand | P22629 |
| B | Streptavidin | protein | 122 | 8% helix, 55% strand | P22629 |
Ligands and binding sites
- SVP · chloro{di-tert-butyl[2-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)ethyl]-lambda~5~-phosphanyl}(1-phenylprop-1-ene-1,3-diyl-kappa~2~C~1~,C~3~)palladium · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.48 | 0.80 | 19 | SVP |
| 2 | 100 | 0.47 | 0.80 | 19 | SVP |
| 3 | 57 | 0.30 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1607 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5CSE · Streptavidin-S112Y-K121E Complexed with Palladium-Containing Biotin Ligand · 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 5CSE · PDBe 5CSE · UniProt P22629
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