MolNFT v1 · #40879 · protein
Candida boidinii formate dehydrogenase (fdh) C-terminal mutant
2J6I: “Candida boidinii formate dehydrogenase (fdh) C-terminal mutant”. X-ray diffraction, 8 pockets (best druggability 0.76). MolNFT v1 #40879 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2J6I
- Type
- protein
- Length
- 1,410 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formate dehydrogenase
- EC
- 1.2.1.2
- UniProt
- O93968
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Formate dehydrogenase (EC 1.2.1.2) | protein | 353 | 39% helix, 18% strand | O93968 |
| C, D | Formate dehydrogenase (EC 1.2.1.2) | protein | 352 | 39% helix, 18% strand | O93968 |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.76 | 0.79 | 91 | empty |
| 2 | 525 | 0.70 | 0.80 | 55 | empty |
| 3 | 555 | 0.70 | 0.79 | 56 | empty |
| 4 | 465 | 0.69 | 0.80 | 48 | empty |
| 5 | 519 | 0.69 | 0.79 | 60 | empty |
Interfaces
5 interfaces between chains.
- B–C · 3191 Ų buried · 59 hydrogen bonds · protein-protein
- A–D · 3184 Ų buried · 57 hydrogen bonds · protein-protein
- A–C · 221 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 80 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 78 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2J6I · Candida boidinii formate dehydrogenase (FDH) C-terminal mutant · 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 O93968
- Elsewhere: RCSB PDB 2J6I · PDBe 2J6I · UniProt O93968
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