MolNFT v1 · #25521 · protein
Streptavidin-cyclo-[5-S-valeramide-HPQGPPC]K-NH2, pH 2.5, I222 complex
1VWJ: “Streptavidin-cyclo-[5-S-valeramide-HPQGPPC]K-NH2, pH 2.5, I222 complex”. X-ray diffraction, 2 ligands (LEA, NH2), 1 pocket (best druggability 0.31). MolNFT v1 #25521 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1VWJ
- Type
- protein
- Length
- 260 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin; Peptide ligand containing hpq
- UniProt
- P22629
- Ligands
- LEA, NH2
- Pockets
- 1 · best druggability 0.31
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Streptavidin | protein | 123 | 8% helix, 58% strand | P22629 |
| D | Streptavidin | protein | 121 | 7% helix, 56% strand | P22629 |
| M, P | Peptide ligand containing hpq | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- LEA · Pentanoic acid · ligand · 2 copies · chains M, P
- NH2 · Amino group · ion · 2 copies · chains M, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.31 | 0.76 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1542 Ų buried · 31 hydrogen bonds · protein-protein
- B–M · 398 Ų buried · 3 hydrogen bonds · protein-protein
- D–P · 397 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1VWJ · Streptavidin-cyclo-[5-S-valeramide-HPQGPPC]K-NH2, pH 2.5, I222 complex · 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 1VWJ · PDBe 1VWJ · UniProt P22629
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