MolNFT v1 · #72416 · protein
NAD-dependent formate dehydrogenase from higher-plant arabidopsis thaliana in complex with NAD and azide
3N7U: “NAD-dependent formate dehydrogenase from higher-plant arabidopsis thaliana in complex with NAD and azide”. X-ray diffraction, 3 ligands (NAD, AZI, SO4), 20 pockets (best druggability 0.78). MolNFT v1 #72416 on GenesisL1: 3D…
- PDB
- 3N7U
- Type
- protein
- Length
- 4,212 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formate dehydrogenase
- EC
- 1.2.1.2
- UniProt
- Q9S7E4
- Ligands
- NAD, AZI, SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Formate dehydrogenase (EC 1.2.1.2) | protein | 351 | 39% helix, 17% strand | Q9S7E4 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- AZI · Azide ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D, F, G, H, I, K
- GOL · Glycerol · additive · 19 copies · chains B, C, E, D, F, G, H, I, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 928 | 0.78 | 0.80 | 101 | empty |
| 2 | 868 | 0.77 | 0.80 | 85 | empty |
| 3 | 373 | 0.76 | 0.86 | 48 | NAD, AZI |
| 4 | 615 | 0.76 | 0.82 | 51 | empty |
| 5 | 375 | 0.75 | 0.86 | 51 | NAD, AZI |
Interfaces
15 interfaces between chains.
- C–D · 3137 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 3124 Ų buried · 45 hydrogen bonds · protein-protein
- K–L · 3087 Ų buried · 46 hydrogen bonds · protein-protein
- I–J · 3068 Ų buried · 45 hydrogen bonds · protein-protein
- G–H · 3058 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 3N7U · NAD-dependent formate dehydrogenase from higher-plant Arabidopsis thaliana in complex… · the same entry in another collection · chain I against I, 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 Q9S7E4
- Elsewhere: RCSB PDB 3N7U · PDBe 3N7U · UniProt Q9S7E4
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