MolNFT v1 · #96565 · protein
Crystal structure of the deph complex with dimethyl-FK228
4JNA: “Crystal structure of the deph complex with dimethyl-FK228”. X-ray diffraction, 6 ligands (1KC, DVA, 060), 4 pockets (best druggability 0.85). MolNFT v1 #96565 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4JNA
- Type
- protein
- Length
- 593 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deph; Dimethyl FK228
- UniProt
- A4ZPY8
- Ligands
- 1KC, DVA, 060, FAD, CL, PO4
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deph | protein | 296 | 28% helix, 32% strand | A4ZPY8 |
| B | Deph | protein | 293 | 28% helix, 31% strand | A4ZPY8 |
| H, I | Dimethyl FK228 | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- 1KC · (3S)-7-methylsulfanyl-3-oxidanyl-hept-4-enoic acid · ligand · 2 copies · chains A, B, H, I
- DVA · D-valine · ligand · 2 copies · chains B, H, A
- 060 · S-methyl-D-cysteine · ligand · 2 copies · chains B, H, A, I
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.85 | 0.88 | 79 | 1KC, DVA, 060, FAD, CL, EDO |
| 2 | 387 | 0.79 | 0.88 | 56 | FAD, CL |
| 3 | 368 | 0.78 | 0.87 | 33 | 1KC, DVA, 060 |
| 4 | 274 | 0.72 | 0.86 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2367 Ų buried · 42 hydrogen bonds · protein-protein
- B–I · 175 Ų buried · 0 hydrogen bonds · protein-protein
- A–H · 166 Ų buried · 0 hydrogen bonds · protein-protein
- A–I · 106 Ų buried · 0 hydrogen bonds · protein-protein
- B–H · 99 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 4JNA · Crystal structure of the DepH complex with dimethyl-FK228 · the same entry in another collection · chain H against H, 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 4JNA · PDBe 4JNA · UniProt A4ZPY8
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