Research workbench
Formate dehydrogenase fdsabg subcomplex fdsbg from C. necator - NADH bound
Analyse Formate dehydrogenase fdsabg subcomplex fdsbg from C. necator - NADH bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VW7
- Type
- protein
- Length
- 1,327 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent formate dehydrogenase gamma subunit; NAD-dependent formate dehydrogenase…
- EC
- 1.2.1.2
- UniProt
- Q0KDY3, Q0KDY2
- Ligands
- FES, FMN, SF4, NAI
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent formate dehydrogenase gamma subunit (EC 1.2.1.2) | protein | 150 | 48% helix, 13% strand | Q0KDY3 |
| B | NAD-dependent formate dehydrogenase beta subunit (EC 1.2.1.2) | protein | 512 | 46% helix, 16% strand | Q0KDY2 |
| C | NAD-dependent formate dehydrogenase gamma subunit (EC 1.2.1.2) | protein | 151 | 46% helix, 13% strand | Q0KDY3 |
| D | NAD-dependent formate dehydrogenase beta subunit (EC 1.2.1.2) | protein | 514 | 46% helix, 17% strand | Q0KDY2 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B, C, D
- FMN · Flavin mononucleotide · ligand · 2 copies · chains B, D
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains B, D
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.74 | 0.82 | 50 | FMN, NAI |
| 2 | 520 | 0.73 | 0.81 | 51 | FMN, NAI |
| 3 | 76 | 0.71 | 0.95 | 22 | empty |
| 4 | 300 | 0.64 | 0.81 | 45 | empty |
| 5 | 269 | 0.62 | 0.81 | 45 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1857 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1836 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 791 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6VW7 · Formate Dehydrogenase FdsABG subcomplex FdsBG from C. necator - NADH bound · 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 Q0KDY3
- Every structure of UniProt Q0KDY2
- Elsewhere: RCSB PDB 6VW7 · PDBe 6VW7 · UniProt Q0KDY3 · UniProt Q0KDY2
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