MolNFT v1 · #143302 · protein
Streptavidin bound to peptide-like compound kpm-6
6AVK: “Streptavidin bound to peptide-like compound kpm-6”. X-ray diffraction, 2 ligands (BZ4, HDO), 2 pockets (best druggability 0.47). MolNFT v1 #143302 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6AVK
- Type
- protein
- Length
- 242 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- BZ4, HDO
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 121 | 7% helix, 56% strand | P22629 |
| B | Streptavidin | protein | 121 | 5% helix, 56% strand | P22629 |
Ligands and binding sites
- BZ4 · N-[(2H-1,3-benzodioxol-5-yl)methyl]-2-({[(2H-1,3-benzodioxol-5-yl)methyl][2-(chloromethyl)-1,3-oxazole-4-carbonyl]amino}methyl)-N-[(4-carbamoyl-1,3-oxazol-2-yl)methyl]-1,3-oxazole-4-carboxamide · ligand · chains A
- HDO · 1-hydroxydodecan-4-one · ligand · chains 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.47 | 0.82 | 17 | HDO |
| 2 | 75 | 0.32 | 0.74 | 15 | BZ4 |
Interfaces
1 interface between chains.
- A–B · 1628 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6AVK · Streptavidin bound to peptide-like compound KPM-6 · the same entry in another collection · chain B against B, 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 6AVK · PDBe 6AVK · UniProt P22629
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