Research workbench
Structure of a dye-linked L-proline dehydrogenase mutant from the aerobic hyperthermophilic archaeon, aeropyrum pernix
Analyse Structure of a dye-linked L-proline dehydrogenase mutant from the aerobic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VQR
- Type
- protein
- Length
- 850 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative oxidoreductase
- UniProt
- Q9YCJ0
- Ligands
- FAD
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative oxidoreductase | protein | 425 | 32% helix, 27% strand | Q9YCJ0 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.86 | 0.87 | 122 | FAD, ACT, EDO |
| 2 | 1116 | 0.86 | 0.86 | 100 | EDO, FAD, ACT |
| 3 | 187 | 0.57 | 0.81 | 26 | empty |
| 4 | 153 | 0.53 | 0.80 | 30 | EDO |
| 5 | 141 | 0.46 | 0.77 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1881 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3VQR · Structure of a dye-linked L-proline dehydrogenase mutant from the aerobic… · 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 3VQR · PDBe 3VQR · UniProt Q9YCJ0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.