Research workbench
Structural basis on the efficient CO2 reduction of acidophilic formate dehydrogenase
Analyse Structural basis on the efficient CO2 reduction of acidophilic formate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WR5
- Type
- protein
- Length
- 1,569 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formate dehydrogenase
- EC
- 1.2.1.2
- UniProt
- Q76EB7
- Ligands
- NAD
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formate dehydrogenase (EC 1.2.1.2) | protein | 401 | 36% helix, 16% strand | Q76EB7 |
| B | Formate dehydrogenase (EC 1.2.1.2) | protein | 395 | 34% helix, 16% strand | Q76EB7 |
| C | Formate dehydrogenase (EC 1.2.1.2) | protein | 397 | 34% helix, 16% strand | Q76EB7 |
| D | Formate dehydrogenase (EC 1.2.1.2) | protein | 376 | 35% helix, 16% strand | Q76EB7 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.76 | 0.85 | 59 | NAD |
| 2 | 389 | 0.76 | 0.86 | 58 | NAD |
| 3 | 449 | 0.75 | 0.84 | 67 | NAD |
| 4 | 1006 | 0.71 | 0.75 | 79 | empty |
| 5 | 464 | 0.69 | 0.80 | 42 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3979 Ų buried · 70 hydrogen bonds · protein-protein
- C–D · 3931 Ų buried · 59 hydrogen bonds · protein-protein
- B–C · 71 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3WR5 · Structural basis on the efficient CO2 reduction of acidophilic formate dehydrogenase · the same entry in another collection · chain B against B, 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 Q76EB7
- Elsewhere: RCSB PDB 3WR5 · PDBe 3WR5 · UniProt Q76EB7
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