MolNFT v1 · #96564 · protein
Crystal structure of the deph
4JN9: “Crystal structure of the deph”. X-ray diffraction, 4 ligands (FAD, MG, CL), 5 pockets (best druggability 0.81). MolNFT v1 #96564 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4JN9
- Type
- protein
- Length
- 593 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deph
- UniProt
- A4ZPY8
- Ligands
- FAD, MG, CL, PO4
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deph | protein | 299 | 28% helix, 30% strand | A4ZPY8 |
| B | Deph | protein | 294 | 28% helix, 33% strand | A4ZPY8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.81 | 0.83 | 82 | EDO, FAD, CL |
| 2 | 1099 | 0.81 | 0.82 | 88 | FAD, CL, EDO |
| 3 | 311 | 0.65 | 0.81 | 32 | empty |
| 4 | 51 | 0.32 | 0.77 | 13 | EDO |
| 5 | 68 | 0.31 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2313 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4JN9 · Crystal structure of the DepH · 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 A4ZPY8
- Elsewhere: RCSB PDB 4JN9 · PDBe 4JN9 · UniProt A4ZPY8
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