Research workbench
Candida boidinii formate dehydrogenase (fdh) K47E mutant
Analyse Candida boidinii formate dehydrogenase (fdh) K47E mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FSS
- Type
- protein
- Length
- 1,389 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formate dehydrogenase
- EC
- 1.2.1.2
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Formate dehydrogenase (EC 1.2.1.2) | protein | 353 | 39% helix, 18% strand | — |
| B | Formate dehydrogenase (EC 1.2.1.2) | protein | 346 | 39% helix, 18% strand | — |
| D | Formate dehydrogenase (EC 1.2.1.2) | protein | 337 | 39% helix, 18% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.77 | 0.80 | 91 | empty |
| 2 | 614 | 0.72 | 0.79 | 64 | SO4 |
| 3 | 556 | 0.71 | 0.80 | 63 | SO4 |
| 4 | 571 | 0.71 | 0.79 | 53 | SO4 |
| 5 | 563 | 0.71 | 0.79 | 63 | empty |
Interfaces
5 interfaces between chains.
- B–C · 3096 Ų buried · 45 hydrogen bonds · protein-protein
- A–D · 2957 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 207 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 142 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 104 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2FSS · Candida boidinii formate dehydrogenase (FDH) K47E 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
- Elsewhere: RCSB PDB 2FSS · PDBe 2FSS
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