Research workbench
6KJ5: Crystal structure of 10-Hydroxygeraniol Dehydrogenase apo form from Cantharanthus roseus
Analyse 6KJ5: Crystal structure of 10-Hydroxygeraniol Dehydrogenase apo form from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KJ5
- Type
- protein
- Length
- 356 residues
- Chains
- 1
- Method
- x-ray diffraction
- Authors
- Sandholu, A.S., Sharmila, P.M., Thulasiram, H.V., Kulkarni, K.A.
- Deposited
- 07/21/19
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.75
- Source
- Catharanthus roseus
- Molecule
- 10-hydroxygeraniol dehydrogenase
- EC
- 1.1.1.324
- UniProt
- Q6V4H0
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · resolution 3.75 · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 10-hydroxygeraniol dehydrogenase (EC 1.1.1.324) | protein | 356 | 30% helix, 27% strand | Q6V4H0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.71 | 0.80 | 59 | empty |
| 2 | 58 | 0.69 | 0.96 | 19 | empty |
| 3 | 54 | 0.27 | 0.73 | 17 | empty |
Compared structures
- 6KJ5 · Crystal structure of 10-hydroxygeraniol dehydrogenase apo form from cantharanthus roseus · the same entry in another collection · chain A against A, TM-score 1.00
- Q6V4H0 · AlphaFold monomer V2.0 prediction for 8-hydroxygeraniol dehydrogenase (Q6V4H0) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q6V4H0
- Elsewhere: RCSB PDB 6KJ5 · PDBe 6KJ5 · UniProt Q6V4H0
Other records of 6KJ5
- 6KJ5-2 · MolNFT v1 / PDB · Crystal structure of 10-hydroxygeraniol dehydrogenase apo form from cantharanthus roseus
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