MolNFT v1 · #127832 · protein
Crystal structure of streptavidin with peptide rdpapawahggg
5N8E: “Crystal structure of streptavidin with peptide rdpapawahggg”. X-ray diffraction, 2 ligands (NA, NH2), 4 pockets (best druggability 0.69). MolNFT v1 #127832 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5N8E
- Type
- protein
- Length
- 516 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin; Arg-asp-pro-ala-pro-ala-TRP-ala-his-gly-gly-gly-NH2
- UniProt
- P22629
- Ligands
- NA, NH2
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 119 | 8% helix, 55% strand | P22629 |
| B | Streptavidin | protein | 122 | 5% helix, 55% strand | P22629 |
| C | Streptavidin | protein | 121 | 7% helix, 55% strand | P22629 |
| D | Streptavidin | protein | 120 | 8% helix, 55% strand | P22629 |
| E | Arg-asp-pro-ala-pro-ala-TRP-ala-his-gly-gly-gly-NH2 | protein | 12 | 33% helix, 0% strand | — |
| F, H | Arg-asp-pro-ala-pro-ala-TRP-ala-his-gly-gly-gly-NH2 | protein | 11 | 36% helix, 0% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains B, C, A, D
- NH2 · Amino group · ion · 3 copies · chains E, A, F, B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.69 | 0.79 | 59 | empty |
| 2 | 362 | 0.64 | 0.79 | 49 | empty |
| 3 | 250 | 0.59 | 0.79 | 40 | empty |
| 4 | 94 | 0.36 | 0.74 | 21 | empty |
Interfaces
13 interfaces between chains.
- B–C · 1595 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 1556 Ų buried · 27 hydrogen bonds · protein-protein
- A–H · 562 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 484 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 481 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5N8E · Crystal structure of streptavidin with peptide rdpapawahggg · 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 5N8E · PDBe 5N8E · UniProt P22629
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.