MolNFT v1 · #177051 · protein
Dehydrogenase holoenzyme
7E5Z · Formate dehydrogenase: “Dehydrogenase holoenzyme”. Electron microscopy, 5 ligands (SF4, MGD, FES), 16 pockets (best druggability 0.80). MolNFT v1 #177051 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7E5Z
- Type
- protein
- Length
- 1,312 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, MGD, FES, FMN, W
- Pockets
- 16 · best druggability 0.80
Structure
electron microscopy · 2 distinct chains · 33% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formate dehydrogenase (EC 1.17.1.9) | protein | 775 | 30% helix, 9% strand | C5ATT7 |
| B | Tungsten-containing formate dehydrogenase beta subunit (EC 1.2.1.2) | protein | 537 | 39% helix, 9% strand | C5ATT6 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 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
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B
- FMN · Flavin mononucleotide · ligand · chains B
- W · Tungsten ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.80 | 0.82 | 84 | FMN |
| 2 | 604 | 0.72 | 0.79 | 90 | W, MGD |
| 3 | 71 | 0.69 | 0.94 | 18 | empty |
| 4 | 53 | 0.69 | 0.96 | 25 | empty |
| 5 | 104 | 0.69 | 0.91 | 32 | SF4 |
Interfaces
1 interface between chains.
- A–B · 2120 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 covalent (covalent ligand).
Compared structures
- 7E5Z · Dehydrogenase holoenzyme · 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 7E5Z · PDBe 7E5Z · UniProt C5ATT7 · UniProt C5ATT6
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