Research workbench
Cryo-EM structure of formate dehydrogenase 1 from methylorubrum extorquens AM1
Analyse Cryo-EM structure of formate dehydrogenase 1 from methylorubrum extorquens AM1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VW6
- Type
- protein
- Length
- 1,473 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formate dehydrogenase; Tungsten-containing formate dehydrogenase beta subunit
- EC
- 1.17.1.9, 1.2.1.2
- UniProt
- C5ATT7, C5ATT6
- Ligands
- SF4, FES, MGD, FMN, W, UNX
- Pockets
- 18 · best druggability 0.89
Structure
electron microscopy · 2 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formate dehydrogenase (EC 1.17.1.9) | protein | 913 | 35% helix, 18% strand | C5ATT7 |
| B | Tungsten-containing formate dehydrogenase beta subunit (EC 1.2.1.2) | protein | 560 | 44% helix, 14% strand | C5ATT6 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 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
- FMN · Flavin mononucleotide · ligand · chains B
- W · Tungsten ion · metal · chains A
- UNX · Unknown atom or ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.89 | 0.96 | 84 | MGD, W, UNX |
| 2 | 781 | 0.83 | 0.86 | 71 | empty |
| 3 | 882 | 0.77 | 0.80 | 80 | FMN |
| 4 | 493 | 0.68 | 0.79 | 33 | empty |
| 5 | 450 | 0.66 | 0.79 | 50 | empty |
Interfaces
1 interface between chains.
- A–B · 3226 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 7VW6 · Cryo-EM Structure of Formate Dehydrogenase 1 from Methylorubrum extorquens AM1 · 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 C5ATT7
- Every structure of UniProt C5ATT6
- Elsewhere: RCSB PDB 7VW6 · PDBe 7VW6 · UniProt C5ATT7 · UniProt C5ATT6
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