Research workbench
The crystal structure of atuah in complex with (S)-ureidoglycolate
Analyse The crystal structure of atuah in complex with (S)-ureidoglycolate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PXB
- Type
- protein
- Length
- 846 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ureidoglycolate hydrolase
- EC
- 3.5.3.19
- UniProt
- Q8VXY9
- Ligands
- UGC, MN
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ureidoglycolate hydrolase (EC 3.5.3.19) | protein | 423 | 38% helix, 25% strand | Q8VXY9 |
Ligands and binding sites
- UGC · (2S)-(carbamoylamino)(hydroxy)ethanoic acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.66 | 0.75 | 101 | empty |
| 2 | 158 | 0.54 | 0.80 | 36 | empty |
| 3 | 170 | 0.53 | 0.79 | 29 | empty |
| 4 | 50 | 0.48 | 0.86 | 20 | empty |
| 5 | 53 | 0.41 | 0.82 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2524 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4PXB · The crystal structure of AtUAH in complex with (S)-ureidoglycolate · the same entry in another collection · chain B against B, TM-score 1.00
- Q8VXY9 · AlphaFold monomer V2.0 prediction for ureidoglycolate hydrolase (Q8VXY9) · a predicted model of the same protein · 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 Q8VXY9
- Elsewhere: RCSB PDB 4PXB · PDBe 4PXB · UniProt Q8VXY9
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