Research workbench
Formaldehyde ferredoxin oxidoreductase from pyrococcus furiosus, complexed with glutarate
Analyse Formaldehyde ferredoxin oxidoreductase from pyrococcus furiosus, complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1B4N
- Type
- protein
- Length
- 2,444 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formaldehyde ferredoxin oxidoreductase
- UniProt
- O93738
- Ligands
- SF4, GUA, PTE, CA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Formaldehyde ferredoxin oxidoreductase | protein | 611 | 44% helix, 14% strand | O93738 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C, D
- GUA · Glutaric acid · ligand · 4 copies · chains A, B, C, D
- PTE · Tungstopterin cofactor · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 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 | 475 | 0.87 | 0.94 | 60 | SF4, GUA, PTE |
| 2 | 455 | 0.87 | 0.94 | 55 | SF4, GUA, PTE |
| 3 | 458 | 0.87 | 0.94 | 57 | SF4, GUA, PTE |
| 4 | 457 | 0.86 | 0.94 | 59 | SF4, GUA, PTE |
| 5 | 187 | 0.49 | 0.76 | 27 | empty |
Interfaces
4 interfaces between chains.
- A–B · 795 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 788 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 786 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 780 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 1B4N · Formaldehyde ferredoxin oxidoreductase from pyrococcus furiosus, complexed with glutarate · 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 1B4N · PDBe 1B4N · UniProt O93738
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