Research workbench
Crystal structure of cordyceps militaris idcase in complex with 5- nitro-uracil
Analyse Crystal structure of cordyceps militaris idcase in complex with 5- nitro-uracil in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HK6
- Type
- protein
- Length
- 1,480 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uracil-5-carboxylate decarboxylase
- EC
- 4.1.1.66
- UniProt
- G3J531
- Ligands
- 5NU, ZN
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Uracil-5-carboxylate decarboxylase (EC 4.1.1.66) | protein | 369 | 47% helix, 15% strand | G3J531 |
| B | Uracil-5-carboxylate decarboxylase (EC 4.1.1.66) | protein | 368 | 48% helix, 13% strand | G3J531 |
| C | Uracil-5-carboxylate decarboxylase (EC 4.1.1.66) | protein | 374 | 49% helix, 13% strand | G3J531 |
Ligands and binding sites
- 5NU · 5-nitrouracil · ligand · 4 copies · chains A, C, B, D
- ZN · Zinc ion · metal · 4 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 | 290 | 0.69 | 0.84 | 40 | empty |
| 2 | 302 | 0.69 | 0.83 | 44 | empty |
| 3 | 247 | 0.67 | 0.83 | 38 | empty |
| 4 | 300 | 0.65 | 0.81 | 46 | empty |
| 5 | 380 | 0.59 | 0.76 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–C · 3058 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 3041 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 28 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4HK6 · Crystal structure of Cordyceps militaris IDCase in complex with 5-nitro-uracil · 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 4HK6 · PDBe 4HK6 · UniProt G3J531
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