Research workbench
Crystal structure of human upar in complex with anti-upar Fab 8B12
Analyse Crystal structure of human upar in complex with anti-upar Fab 8B12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QTI
- Type
- protein
- Length
- 690 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-upar antibody, heavy chain; Anti-upar antibody, light chain; Urokinase plasminogen…
- UniProt
- Q03405
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Anti-upar antibody, heavy chain | protein | 218 | 8% helix, 53% strand | — |
| L | Anti-upar antibody, light chain | protein | 212 | 6% helix, 50% strand | — |
| U | Urokinase plasminogen activator surface receptor | protein | 260 | 5% helix, 48% strand | Q03405 |
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 | 318 | 0.61 | 0.78 | 33 | empty |
| 2 | 362 | 0.54 | 0.74 | 53 | empty |
| 3 | 128 | 0.40 | 0.75 | 24 | empty |
| 4 | 58 | 0.28 | 0.73 | 12 | empty |
| 5 | 63 | 0.27 | 0.72 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1753 Ų buried · 20 hydrogen bonds · protein-protein
- L–U · 432 Ų buried · 7 hydrogen bonds · protein-protein
- H–U · 381 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 4QTI · Crystal structure of human uPAR in complex with anti-uPAR Fab 8B12 · the same entry in another collection · chain H against H, 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 0.98
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
- Elsewhere: RCSB PDB 4QTI · PDBe 4QTI · UniProt Q03405
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