MolNFT v1 · #21787 · protein
Streptavidin, pH 5.0, bound to cyclic peptide ac-chpqgppc- NH2
1SLE: “Streptavidin, pH 5.0, bound to cyclic peptide ac-chpqgppc- NH2”. X-ray diffraction, 2 ligands (ACE, NH2), 2 pockets (best druggability 0.31). MolNFT v1 #21787 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1SLE
- Type
- protein
- Length
- 258 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin; Ac-chpqgppc-NH2
- UniProt
- P22629
- Ligands
- ACE, NH2
- Pockets
- 2 · best druggability 0.31
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Streptavidin | protein | 121 | 8% helix, 57% strand | P22629 |
| M, P | Ac-chpqgppc-NH2 | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · 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
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 | 52 | 0.31 | 0.77 | 11 | empty |
| 2 | 53 | 0.30 | 0.77 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1593 Ų buried · 20 hydrogen bonds · protein-protein
- B–M · 393 Ų buried · 2 hydrogen bonds · protein-protein
- D–P · 380 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 1SLE · Streptavidin, pH 5.0, bound to cyclic peptide ac-chpqgppc-NH2 · 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 1SLE · PDBe 1SLE · UniProt P22629
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