Research workbench
Formate dehydrogenase N from E. COLI
Analyse Formate dehydrogenase N from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KQF
- Type
- protein
- Length
- 1,487 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formate dehydrogenase, nitrate-inducible, major subunit; Formate dehydrogenase…
- EC
- 1.2.1.2
- UniProt
- P24183, P0AAJ3, P24185
- Ligands
- SF4, MGD, HEM, CDL, 6MO
- Pockets
- 15 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formate dehydrogenase, nitrate-inducible, major subunit (EC 1.2.1.2) | protein | 982 | 30% helix, 19% strand | P24183 |
| B | Formate dehydrogenase, nitrate-inducible, iron-sulfur subunit (EC 1.2.1.2) | protein | 289 | 29% helix, 19% strand | P0AAJ3 |
| C | Formate dehydrogenase, nitrate-inducible, cytochrome B556(FDN) subunit (EC 1.2.1.2) | protein | 216 | 76% helix, 3% strand | P24185 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 5 copies · chains A, B
- MGD · 2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-anthracen-4-one guanosine dinucleotide · ligand · 2 copies · chains A
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains B, C
- CDL · Cardiolipin · ligand · chains B, C
- 6MO · Molybdenum(vi) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.89 | 0.95 | 90 | 6MO, MGD |
| 2 | 284 | 0.84 | 0.94 | 40 | HEM |
| 3 | 647 | 0.81 | 0.85 | 67 | HEM |
| 4 | 941 | 0.75 | 0.78 | 82 | empty |
| 5 | 181 | 0.56 | 0.81 | 38 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2568 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 1945 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
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 P24183
- Every structure of UniProt P0AAJ3
- Every structure of UniProt P24185
- Elsewhere: RCSB PDB 1KQF · PDBe 1KQF · UniProt P24183 · UniProt P0AAJ3 · UniProt P24185
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