Research workbench
Structure of anti-upar Fab atn-658 in complex with upar
Analyse Structure of anti-upar Fab atn-658 in complex with upar in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K24
- Type
- protein
- Length
- 868 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urokinase-type plasminogen activator; Vitronectin; Anti-upar antibody, heavy chain…
- EC
- 3.4.21.73
- UniProt
- P00749, P04004, Q03405
- Ligands
- NAG, MAN
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 125 | 9% helix, 17% strand | P00749 |
| B | Vitronectin | protein | 40 | 20% helix, 0% strand | P04004 |
| H | Anti-upar antibody, heavy chain | protein | 212 | 6% helix, 47% strand | — |
| L | Anti-upar antibody, light chain | protein | 218 | 6% helix, 44% strand | — |
| U | Urokinase plasminogen activator surface receptor | protein | 273 | 4% helix, 40% strand | Q03405 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains U
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.69 | 0.82 | 55 | empty |
| 2 | 287 | 0.68 | 0.83 | 44 | empty |
| 3 | 448 | 0.66 | 0.79 | 52 | empty |
| 4 | 86 | 0.63 | 0.90 | 28 | empty |
| 5 | 90 | 0.59 | 0.87 | 20 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1944 Ų buried · 20 hydrogen bonds · protein-protein
- A–U · 1394 Ų buried · 24 hydrogen bonds · protein-protein
- B–U · 596 Ų buried · 9 hydrogen bonds · protein-protein
- H–U · 471 Ų buried · 7 hydrogen bonds · protein-protein
- L–U · 108 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 4 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 4K24 · Structure of anti-uPAR Fab ATN-658 in complex with uPAR · the same entry in another collection · chain B against B, 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 0.96
- P04004 · AlphaFold monomer V2.0 prediction for vitronectin (P04004) · a predicted model of the same protein · chain B against A, TM-score 0.74
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 P04004
- Every structure of UniProt Q03405
- Elsewhere: RCSB PDB 4K24 · PDBe 4K24 · UniProt P00749 · UniProt P04004 · UniProt Q03405
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