Research workbench
X-ray analyses of 3-hydroxybutyrate dehydrogenase from alcaligenes faecalis
Analyse X-ray analyses of 3-hydroxybutyrate dehydrogenase from alcaligenes faecalis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YZ7
- Type
- protein
- Length
- 2,080 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-3-hydroxybutyrate dehydrogenase
- EC
- 1.1.1.30
- Ligands
- CA, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | D-3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) | protein | 260 | 51% helix, 13% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, C, B, D, E, G, F, H
- CL · Chloride ion · ion · 8 copies · chains A, D, B, C, E, G, H, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.85 | 0.87 | 59 | CA |
| 2 | 936 | 0.85 | 0.87 | 57 | CA |
| 3 | 580 | 0.71 | 0.79 | 57 | CL |
| 4 | 383 | 0.69 | 0.82 | 42 | empty |
| 5 | 524 | 0.68 | 0.78 | 55 | CL |
Interfaces
12 interfaces between chains.
- A–D · 1496 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1483 Ų buried · 13 hydrogen bonds · protein-protein
- F–G · 1482 Ų buried · 13 hydrogen bonds · protein-protein
- E–H · 1464 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 1263 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2YZ7 · X-ray analyses of 3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis · the same entry in another collection · chain H against H, 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
- Elsewhere: RCSB PDB 2YZ7 · PDBe 2YZ7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.