MolNFT v1 · #58241 · protein
Structure of a dye-linked L-proline dehydrogenase from the aerobic hyperthermophilic archaeon, aeropyrum pernix
3AXB · Putative oxidoreductase: “Structure of a dye-linked L-proline dehydrogenase from the aerobic hyperthermophilic archaeon, aeropyrum…”. X-ray diffraction, 2 ligands (PRO, FAD), 5 pockets (best druggability 0.82). MolNFT v1 #58241 on…
- PDB
- 3AXB
- Type
- protein
- Length
- 428 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative oxidoreductase
- UniProt
- Q9YCJ0
- Ligands
- PRO, FAD
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative oxidoreductase | protein | 428 | 31% helix, 27% strand | Q9YCJ0 |
Ligands and binding sites
- PRO · Proline · ligand · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.82 | 0.90 | 61 | PRO, FAD |
| 2 | 93 | 0.38 | 0.76 | 21 | EDO |
| 3 | 105 | 0.36 | 0.74 | 23 | empty |
| 4 | 72 | 0.35 | 0.76 | 16 | empty |
| 5 | 64 | 0.30 | 0.75 | 13 | empty |
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3AXB · Structure of a dye-linked L-proline dehydrogenase from the aerobic hyperthermophilic… · 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 Q9YCJ0
- Elsewhere: RCSB PDB 3AXB · PDBe 3AXB · UniProt Q9YCJ0
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