Research workbench
Crystal structure of formaldehyde dehydrogenase from pseudomonas aeruginosa
Analyse Crystal structure of formaldehyde dehydrogenase from pseudomonas aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JLW
- Type
- protein
- Length
- 1,580 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione-independent formaldehyde dehydrogenase
- UniProt
- B7V5W2
- Ligands
- NAD, ZN, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glutathione-independent formaldehyde dehydrogenase | protein | 395 | 31% helix, 24% strand | B7V5W2 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.80 | 0.95 | 27 | empty |
| 2 | 227 | 0.80 | 0.93 | 30 | empty |
| 3 | 400 | 0.79 | 0.88 | 51 | ZN, NAD |
| 4 | 385 | 0.79 | 0.88 | 50 | NAD |
| 5 | 378 | 0.79 | 0.88 | 51 | NAD |
Interfaces
6 interfaces between chains.
- C–D · 1726 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1709 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 896 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 887 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 799 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4JLW · Crystal structure of formaldehyde dehydrogenase from Pseudomonas aeruginosa · the same entry in another collection · chain D against D, 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 B7V5W2
- Elsewhere: RCSB PDB 4JLW · PDBe 4JLW · UniProt B7V5W2
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