MolNFT v1 · #58474 · protein
FGD1 (RV0407) from mycobacterium tuberculosis
3B4Y · Probable F420-dependent glucose-6-phosphate dehydrogenase…: “FGD1 (RV0407) from mycobacterium tuberculosis”. X-ray diffraction, 1 ligand (F42), 4 pockets (best druggability 0.78). MolNFT v1 #58474 on GenesisL1: 3D structure, binding…
- PDB
- 3B4Y
- Type
- protein
- Length
- 664 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable F420-dependent glucose-6-phosphate dehydrogenase FGD1
- EC
- 1.-.-.-
- UniProt
- P96253
- Ligands
- F42
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable F420-dependent glucose-6-phosphate dehydrogenase FGD1 (EC 1.-.-.-) | protein | 332 | 46% helix, 17% strand | P96253 |
Ligands and binding sites
- F42 · Coenzyme F420 · ligand · 2 copies · chains A, B
- FLC · Citrate anion · additive · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.78 | 0.88 | 38 | F42, FLC |
| 2 | 369 | 0.76 | 0.87 | 38 | F42, FLC |
| 3 | 420 | 0.67 | 0.79 | 46 | empty |
| 4 | 52 | 0.28 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2077 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered, oxidation).
Compared structures
- 3B4Y · FGD1 (Rv0407) from Mycobacterium tuberculosis · 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 P96253
- Elsewhere: RCSB PDB 3B4Y · PDBe 3B4Y · UniProt P96253
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