MolNFT v1 · #98475 · protein
Crystal structure of cordyceps militaris idcase D323N mutant in complex with 5-carboxyl-uracil
4LAM · Uracil-5-carboxylate decarboxylase: “Crystal structure of cordyceps militaris idcase D323N mutant in complex with 5-carboxyl-uracil”. X-ray diffraction, 2 ligands (5CU, ZN), 10 pockets (best druggability 0.69). MolNFT v1 #98475 on…
- PDB
- 4LAM
- Type
- protein
- Length
- 732 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uracil-5-carboxylate decarboxylase
- UniProt
- G3J531
- Ligands
- 5CU, ZN
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uracil-5-carboxylate decarboxylase | protein | 365 | 49% helix, 13% strand | G3J531 |
| B | Uracil-5-carboxylate decarboxylase | protein | 367 | 49% helix, 13% strand | G3J531 |
Ligands and binding sites
- 5CU · 2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- P6G · Hexaethylene glycol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.69 | 0.86 | 42 | empty |
| 2 | 217 | 0.67 | 0.84 | 44 | empty |
| 3 | 150 | 0.49 | 0.78 | 21 | empty |
| 4 | 109 | 0.48 | 0.80 | 19 | P6G |
| 5 | 151 | 0.47 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3008 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4LAM · Crystal structure of Cordyceps militaris IDCase D323N mutant in complex with… · 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 4LAM · PDBe 4LAM · UniProt G3J531
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