MolNFT v1 · #45687 · protein
High resolution structures of holo and apo formate dehydrogenase
2NAD · NAD-dependent formate dehydrogenase: “High resolution structures of holo and apo formate dehydrogenase”. X-ray diffraction, 3 ligands (NAD, AZI, SO4), 8 pockets (best druggability 0.77). MolNFT v1 #45687 on GenesisL1: 3D structure…
- PDB
- 2NAD
- Type
- protein
- Length
- 774 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent formate dehydrogenase
- EC
- 1.2.1.2
- UniProt
- P33160
- Ligands
- NAD, AZI, SO4
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent formate dehydrogenase (EC 1.2.1.2) | protein | 391 | 34% helix, 17% strand | P33160 |
| B | NAD-dependent formate dehydrogenase (EC 1.2.1.2) | protein | 383 | 35% helix, 16% strand | P33160 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- AZI · Azide ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.77 | 0.87 | 58 | AZI, NAD |
| 2 | 414 | 0.75 | 0.85 | 58 | AZI, NAD |
| 3 | 173 | 0.54 | 0.79 | 28 | empty |
| 4 | 216 | 0.49 | 0.76 | 39 | empty |
| 5 | 122 | 0.48 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3911 Ų buried · 59 hydrogen bonds · protein-protein
Compared structures
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 P33160
- Elsewhere: RCSB PDB 2NAD · PDBe 2NAD · UniProt P33160
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