MolNFT v1 · #1446 · protein
Formaldehyde ferredoxin oxidoreductase from pyrococcus furiosus
1B25 · Protein (formaldehyde ferredoxin oxidoreductase): “Formaldehyde ferredoxin oxidoreductase from pyrococcus furiosus”. X-ray diffraction, 2 ligands (SF4, PTT), 20 pockets (best druggability 0.87). MolNFT v1 #1446 on GenesisL1: 3D…
- PDB
- 1B25
- Type
- protein
- Length
- 2,444 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (formaldehyde ferredoxin oxidoreductase)
- UniProt
- O93738
- Ligands
- SF4, PTT
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protein (formaldehyde ferredoxin oxidoreductase) | protein | 611 | 45% helix, 14% strand | O93738 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C, D
- PTT · Tungstopterin · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.87 | 0.94 | 61 | SF4, PTT |
| 2 | 462 | 0.87 | 0.94 | 61 | SF4, PTT |
| 3 | 456 | 0.87 | 0.94 | 58 | SF4, PTT |
| 4 | 457 | 0.86 | 0.94 | 58 | SF4, PTT |
| 5 | 174 | 0.49 | 0.77 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–D · 818 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 799 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 799 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 787 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 1B25 · Formaldehyde ferredoxin oxidoreductase from pyrococcus furiosus · the same entry in another collection · chain B against B, 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 O93738
- Elsewhere: RCSB PDB 1B25 · PDBe 1B25 · UniProt O93738
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