Research workbench
Crystal structure of Cordyceps militaris IDCase D323N mutant in apo form
Analyse Crystal structure of Cordyceps militaris IDCase D323N mutant in apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LAK
- Type
- protein
- Length
- 698 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.41
- Source
- Cordyceps militaris
- Molecule
- Uracil-5-carboxylate decarboxylase
- UniProt
- G3J531
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.41 · 2 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uracil-5-carboxylate decarboxylase | protein | 336 | 50% helix, 12% strand | G3J531 |
| B | Uracil-5-carboxylate decarboxylase | protein | 362 | 50% helix, 14% strand | G3J531 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.77 | 0.87 | 51 | empty |
| 2 | 561 | 0.69 | 0.78 | 47 | empty |
| 3 | 197 | 0.51 | 0.77 | 29 | empty |
| 4 | 115 | 0.50 | 0.80 | 19 | empty |
| 5 | 100 | 0.44 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2836 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4LAK · Crystal structure of cordyceps militaris idcase D323N mutant in apo form · 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 G3J531
- Elsewhere: RCSB PDB 4LAK · PDBe 4LAK · UniProt G3J531
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