MolNFT v1 · #28834 · protein
Crystal structure of ureidoglycolate hydrolase (alla) from escherichia COLI O157:H7
1YQC: “Crystal structure of ureidoglycolate hydrolase (alla) from escherichia COLI O157:H7”. X-ray diffraction, 1 ligand (GLV), 3 pockets (best druggability 0.63). MolNFT v1 #28834 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1YQC
- Type
- protein
- Length
- 320 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ureidoglycolate hydrolase
- EC
- 3.5.3.19
- UniProt
- P63486
- Ligands
- GLV
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ureidoglycolate hydrolase (EC 3.5.3.19) | protein | 160 | 4% helix, 50% strand | P63486 |
Ligands and binding sites
- GLV · Glyoxylic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.63 | 0.85 | 27 | GLV |
| 2 | 216 | 0.63 | 0.82 | 38 | empty |
| 3 | 50 | 0.27 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1987 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 1YQC · Crystal Structure of Ureidoglycolate Hydrolase (AllA) from Escherichia coli O157:H7 · the same entry in another collection · chain A against A, TM-score 1.00
- P63486 · AlphaFold monomer V2.0 prediction for ureidoglycolate lyase (P63486) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P63486
- Elsewhere: RCSB PDB 1YQC · PDBe 1YQC · UniProt P63486
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