MolNFT v1 · #127815 · protein
Crystal structure of streptavidin with peptide ewvhpqfeqkak
5N7X: “Crystal structure of streptavidin with peptide ewvhpqfeqkak”. X-ray diffraction, 12 pockets (best druggability 0.72). MolNFT v1 #127815 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5N7X
- Type
- protein
- Length
- 1,062 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin; Glu-TRP-val-his-pro-gln-phe-glu-gln-lys-ala-lys peptide
- UniProt
- P22629
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F, H, K, O | Streptavidin | protein | 122 | 7% helix, 55% strand | P22629 |
| B, M | Streptavidin | protein | 121 | 7% helix, 55% strand | P22629 |
| C, D, G, I, J, L, N, P | Glu-TRP-val-his-pro-gln-phe-glu-gln-lys-ala-lys peptide | protein | 11 | 0% helix, 0% strand | — |
Pockets
12 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.72 | 0.80 | 63 | empty |
| 2 | 612 | 0.71 | 0.79 | 57 | empty |
| 3 | 281 | 0.61 | 0.79 | 29 | empty |
| 4 | 258 | 0.60 | 0.80 | 33 | empty |
| 5 | 307 | 0.60 | 0.79 | 31 | empty |
Interfaces
29 interfaces between chains.
- K–O · 1628 Ų buried · 26 hydrogen bonds · protein-protein
- A–E · 1619 Ų buried · 25 hydrogen bonds · protein-protein
- H–M · 1613 Ų buried · 26 hydrogen bonds · protein-protein
- B–F · 1610 Ų buried · 25 hydrogen bonds · protein-protein
- H–J · 544 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5N7X · Crystal structure of streptavidin with peptide ewvhpqfeqkak · 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 5N7X · PDBe 5N7X · UniProt P22629
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