MolNFT v1 · #72509 · protein
Apo-form of NAD-dependent formate dehydrogenase from higher-plant arabidopsis thaliana
3NAQ: “Apo-form of NAD-dependent formate dehydrogenase from higher-plant arabidopsis thaliana”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.67). MolNFT v1 #72509 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3NAQ
- Type
- protein
- Length
- 702 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formate dehydrogenase
- EC
- 1.2.1.2
- UniProt
- Q9S7E4
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Formate dehydrogenase (EC 1.2.1.2) | protein | 351 | 39% helix, 17% strand | Q9S7E4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 636 | 0.67 | 0.76 | 69 | empty |
| 2 | 590 | 0.66 | 0.76 | 50 | empty |
| 3 | 247 | 0.55 | 0.77 | 39 | SO4 |
| 4 | 224 | 0.53 | 0.77 | 39 | SO4 |
Interfaces
1 interface between chains.
- A–B · 3061 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 3NAQ · Apo-form of NAD-dependent formate dehydrogenase from higher-plant Arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00
- Q9S7E4 · AlphaFold monomer V2.0 prediction for formate dehydrogenase, CHLOROPLASTIC/MITOCHONDRIAL… · a predicted model of the same protein · chain B against A, TM-score 0.92
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 Q9S7E4
- Elsewhere: RCSB PDB 3NAQ · PDBe 3NAQ · UniProt Q9S7E4
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