MolNFT v1 · #123315 · protein
Crystal structure of the de novo mini protein GEHEE_06
5JG9 · De novo design, hyper stable, disulfide-rich mini protein: “Crystal structure of the de novo mini protein GEHEE_06”. X-ray diffraction, 1 ligand (CL), 1 pocket (best druggability 0.45). MolNFT v1 #123315 on GenesisL1: 3D structure…
- PDB
- 5JG9
- Type
- protein
- Length
- 140 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- De novo design, hyper stable, disulfide-rich mini protein
- Ligands
- CL
- Pockets
- 1 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | De novo design, hyper stable, disulfide-rich mini protein | protein | 46 | 33% helix, 43% strand | — |
| B, C | De novo design, hyper stable, disulfide-rich mini protein | protein | 47 | 30% helix, 45% strand | — |
Ligands and binding sites
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 | 100 | 0.45 | 0.80 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 403 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 364 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 99 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 5JG9 · Crystal structure of the de novo mini protein gEHEE_06 · 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
- Elsewhere: RCSB PDB 5JG9 · PDBe 5JG9
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