MolNFT v1 · #127829 · protein
Crystal structure of streptavidin with peptide afpdylaeyhgg
5N8B: “Crystal structure of streptavidin with peptide afpdylaeyhgg”. X-ray diffraction, 1 ligand (NH2), 4 pockets (best druggability 0.69). MolNFT v1 #127829 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5N8B
- Type
- protein
- Length
- 535 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin; Ala-phe-pro-asp-tyr-leu-ala-glu-tyr-his-gly-gly-NH2
- UniProt
- P22629
- Ligands
- NH2
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Streptavidin | protein | 121 | 7% helix, 55% strand | P22629 |
| E, C, F, H | Ala-phe-pro-asp-tyr-leu-ala-glu-tyr-his-gly-gly-NH2 | protein | 12 | 50% helix, 0% strand | — |
| B | Streptavidin | protein | 120 | 8% helix, 55% strand | P22629 |
| D | Streptavidin | protein | 125 | 10% helix, 53% strand | P22629 |
Ligands and binding sites
- NH2 · Amino group · ion · 4 copies · chains A, E, B, C, D, F, G, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.69 | 0.79 | 67 | empty |
| 2 | 499 | 0.67 | 0.79 | 64 | empty |
| 3 | 104 | 0.35 | 0.73 | 20 | empty |
| 4 | 68 | 0.29 | 0.73 | 18 | empty |
Interfaces
14 interfaces between chains.
- A–D · 1631 Ų buried · 24 hydrogen bonds · protein-protein
- B–G · 1605 Ų buried · 22 hydrogen bonds · protein-protein
- D–F · 692 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 692 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 686 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5N8B · Crystal structure of streptavidin with peptide afpdylaeyhgg · 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 5N8B · PDBe 5N8B · UniProt P22629
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