Research workbench
NAD-dependent formate dehydrogenase from pseudomonas SP.101 in complex with formate
Analyse NAD-dependent formate dehydrogenase from pseudomonas SP.101 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GUG
- Type
- protein
- Length
- 1,468 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formate dehydrogenase
- EC
- 1.2.1.2
- UniProt
- P33160
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formate dehydrogenase (EC 1.2.1.2) | protein | 368 | 34% helix, 18% strand | P33160 |
| B, C | Formate dehydrogenase (EC 1.2.1.2) | protein | 369 | 34% helix, 16% strand | P33160 |
| D | Formate dehydrogenase (EC 1.2.1.2) | protein | 362 | 35% helix, 17% strand | P33160 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, C, B
- FMT · Formic acid · additive · 3 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.70 | 0.84 | 45 | FMT, PEG |
| 2 | 499 | 0.70 | 0.80 | 50 | FMT |
| 3 | 528 | 0.70 | 0.80 | 55 | FMT |
| 4 | 303 | 0.67 | 0.82 | 38 | empty |
| 5 | 310 | 0.56 | 0.76 | 52 | PG4 |
Interfaces
3 interfaces between chains.
- A–C · 3903 Ų buried · 65 hydrogen bonds · protein-protein
- B–D · 3871 Ų buried · 67 hydrogen bonds · protein-protein
- A–D · 334 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 2GUG · NAD-dependent formate dehydrogenase from Pseudomonas sp.101 in complex with formate · the same entry in another collection · chain D against D, TM-score 1.00
- P33160 · AlphaFold monomer V2.0 prediction for formate dehydrogenase (P33160) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 2GUG · PDBe 2GUG · UniProt P33160
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