MolNFT v1 · #123294 · protein
Crystal structure of rhodopseudomonas palustris propionaldehyde dehydrogenase with bound CoA and acylated CYS330
5JFN: “Crystal structure of rhodopseudomonas palustris propionaldehyde dehydrogenase with bound CoA and acylated…”. X-ray diffraction, 2 ligands (COA, 1VU), 18 pockets (best druggability 0.79). MolNFT v1 #123294 on GenesisL1: 3D structure…
- PDB
- 5JFN
- Type
- protein
- Length
- 1,763 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase
- UniProt
- Q21A49
- Ligands
- COA, 1VU
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Aldehyde dehydrogenase | protein | 439 | 45% helix, 21% strand | Q21A49 |
| C | Aldehyde dehydrogenase | protein | 446 | 44% helix, 20% strand | Q21A49 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 3 copies · chains B, C, D
- 1VU · propionyl Coenzyme A · ligand · chains A
- 1PE · Pentaethylene glycol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.79 | 0.89 | 46 | empty |
| 2 | 336 | 0.79 | 0.90 | 40 | empty |
| 3 | 262 | 0.61 | 0.80 | 45 | COA |
| 4 | 344 | 0.60 | 0.77 | 45 | empty |
| 5 | 241 | 0.59 | 0.79 | 39 | 1VU |
Interfaces
6 interfaces between chains.
- B–D · 2648 Ų buried · 61 hydrogen bonds · protein-protein
- A–C · 2594 Ų buried · 60 hydrogen bonds · protein-protein
- C–D · 1287 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1229 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 588 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 1 covalent (nonstandard, covalent ligand).
Compared structures
- 5JFN · Crystal structure of Rhodopseudomonas palustris propionaldehyde dehydrogenase with bound… · 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 Q21A49
- Elsewhere: RCSB PDB 5JFN · PDBe 5JFN · UniProt Q21A49
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