Research workbench
Crystal structure of stabilized human uPAR mutant in complex with ATF
Analyse Crystal structure of stabilized human uPAR mutant in complex with ATF in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U73
- Type
- protein
- Length
- 392 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.19
- Source
- Homo sapiens
- Molecule
- Urokinase plasminogen activator surface receptor; Urokinase-type plasminogen activator
- EC
- 3.4.21.73
- UniProt
- Q03405, P00749
- Ligands
- NAG, MAN
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · resolution 3.19 · 2 distinct chains · 6% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| U | Urokinase plasminogen activator surface receptor | protein | 269 | 6% helix, 48% strand | Q03405 |
| A | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 123 | 6% helix, 21% strand | P00749 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains U
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 394 | 0.65 | 0.79 | 51 | empty |
| 2 | 302 | 0.53 | 0.74 | 36 | empty |
| 3 | 112 | 0.36 | 0.73 | 19 | empty |
| 4 | 105 | 0.36 | 0.74 | 15 | empty |
| 5 | 68 | 0.33 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- U–A · 1336 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3U73 · Crystal structure of stabilized human upar mutant in complex with atf · the same entry in another collection · chain A against A, TM-score 1.00
- Q03405 · AlphaFold monomer V2.0 prediction for urokinase plasminogen activator surface receptor… · a predicted model of the same protein · chain U against A, TM-score 0.97
- P00749 · AlphaFold monomer V2.0 prediction for urokinase-type plasminogen activator (P00749) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q03405
- Every structure of UniProt P00749
- Elsewhere: RCSB PDB 3U73 · PDBe 3U73 · UniProt Q03405 · UniProt P00749
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