Research workbench
Crystal structure of ATF-urokinase receptor complex
Analyse Crystal structure of ATF-urokinase receptor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2I9B
- Type
- protein
- Length
- 1,514 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Homo sapiens
- Molecule
- Urokinase-type plasminogen activator; Urokinase plasminogen activator surface receptor
- EC
- 3.4.21.73
- UniProt
- P00749, Q03405
- Ligands
- NAG, BMA, SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.8 · 3 distinct chains · 3% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 122 | 6% helix, 25% strand | P00749 |
| E, F | Urokinase plasminogen activator surface receptor | protein | 265 | 1% helix, 46% strand | Q03405 |
| G, H | Urokinase plasminogen activator surface receptor | protein | 248 | 2% helix, 45% strand | Q03405 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains E, F, G, H
- BMA · beta-D-mannopyranose · sugar · 2 copies
- SO4 · Sulfate ion · ion · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 789 | 0.78 | 0.82 | 87 | empty |
| 2 | 961 | 0.78 | 0.80 | 94 | empty |
| 3 | 766 | 0.75 | 0.80 | 96 | empty |
| 4 | 50 | 0.69 | 0.97 | 23 | empty |
| 5 | 457 | 0.67 | 0.79 | 59 | empty |
Interfaces
11 interfaces between chains.
- B–F · 1282 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 1280 Ų buried · 11 hydrogen bonds · protein-protein
- C–G · 1252 Ų buried · 11 hydrogen bonds · protein-protein
- D–H · 1244 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 521 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 80 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 2I9B · Crystal structure of atf-urokinase receptor complex · the same entry in another collection · chain H against H, TM-score 1.00
- 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 0.98
- Q03405 · AlphaFold monomer V2.0 prediction for urokinase plasminogen activator surface receptor… · a predicted model of the same protein · chain G 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 P00749
- Every structure of UniProt Q03405
- Elsewhere: RCSB PDB 2I9B · PDBe 2I9B · UniProt P00749 · UniProt Q03405
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