MolNFT v1 · #116753 · protein
Crystal structure of candida boidinii formate dehydrogenase complexed with NAD+ and azide
5DN9 · Fdh: “Crystal structure of candida boidinii formate dehydrogenase complexed with NAD+ and azide”. X-ray diffraction, 3 ligands (NAD, AZI, CL), 4 pockets (best druggability 0.74). MolNFT v1 #116753 on GenesisL1: 3D structure, binding…
- PDB
- 5DN9
- Type
- protein
- Length
- 722 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fdh
- EC
- 1.2.1.2
- UniProt
- A0A0A1EQY0
- Ligands
- NAD, AZI, CL
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fdh (EC 1.2.1.2) | protein | 361 | 38% helix, 18% strand | A0A0A1EQY0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- AZI · Azide ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 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 | 362 | 0.74 | 0.85 | 55 | NAD, AZI, CL |
| 2 | 358 | 0.74 | 0.85 | 51 | NAD, AZI, CL |
| 3 | 191 | 0.56 | 0.80 | 30 | empty |
| 4 | 153 | 0.55 | 0.81 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 3224 Ų buried · 57 hydrogen bonds · protein-protein
Compared structures
- 5DN9 · Crystal structure of Candida boidinii formate dehydrogenase complexed with NAD+ and azide · 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 A0A0A1EQY0
- Elsewhere: RCSB PDB 5DN9 · PDBe 5DN9 · UniProt A0A0A1EQY0
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