Research workbench
The crystal structure of probable ornithine cyclodeaminase from bordetella pertussis tohama I
Analyse The crystal structure of probable ornithine cyclodeaminase from bordetella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HDJ
- Type
- protein
- Length
- 622 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ornithine cyclodeaminase
- UniProt
- Q7VSP8
- Ligands
- CL
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable ornithine cyclodeaminase | protein | 311 | 41% helix, 26% strand | Q7VSP8 |
Ligands and binding sites
- CL · Chloride ion · ion · 7 copies · chains A, B
- IMD · Imidazole · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 390 | 0.68 | 0.81 | 45 | CL |
| 2 | 384 | 0.66 | 0.80 | 47 | CL, GOL |
Interfaces
1 interface between chains.
- A–B · 1499 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3HDJ · The crystal structure of probable ornithine cyclodeaminase from Bordetella pertussis… · 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 Q7VSP8
- Elsewhere: RCSB PDB 3HDJ · PDBe 3HDJ · UniProt Q7VSP8
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