Research workbench
Crystal structure of Cordyceps militaris IDCase in apo form
Analyse Crystal structure of Cordyceps militaris IDCase 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
- 4HK5
- Type
- protein
- Length
- 1,470 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Cordyceps militaris
- Molecule
- Uracil-5-carboxylate decarboxylase
- EC
- 4.1.1.66
- UniProt
- G3J531
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · resolution 1.9 · 4 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uracil-5-carboxylate decarboxylase (EC 4.1.1.66) | protein | 358 | 49% helix, 14% strand | G3J531 |
| B | Uracil-5-carboxylate decarboxylase (EC 4.1.1.66) | protein | 362 | 48% helix, 14% strand | G3J531 |
| C | Uracil-5-carboxylate decarboxylase (EC 4.1.1.66) | protein | 370 | 48% helix, 13% strand | G3J531 |
| D | Uracil-5-carboxylate decarboxylase (EC 4.1.1.66) | protein | 380 | 49% helix, 14% strand | G3J531 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.70 | 0.84 | 45 | empty |
| 2 | 236 | 0.67 | 0.84 | 40 | empty |
| 3 | 241 | 0.63 | 0.81 | 36 | empty |
| 4 | 216 | 0.62 | 0.82 | 37 | empty |
| 5 | 145 | 0.51 | 0.79 | 20 | empty |
Interfaces
2 interfaces between chains.
- B–D · 3008 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 3007 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4HK5 · Crystal structure of cordyceps militaris idcase 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 4HK5 · PDBe 4HK5 · UniProt G3J531
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