Research workbench
The crystal structure of upa in complex with the Fab fragment of mab- 112
Analyse The crystal structure of upa in complex with the Fab fragment of mab- 112 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DW2
- Type
- protein
- Length
- 645 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urokinase-type plasminogen activator; Fab fragment of pro-upa antibody mab-112
- EC
- 3.4.21.73
- UniProt
- P00749
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| U | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 221 | 5% helix, 35% strand | P00749 |
| H | Fab fragment of pro-upa antibody mab-112 | protein | 210 | 3% helix, 47% strand | — |
| L | Fab fragment of pro-upa antibody mab-112 | protein | 214 | 7% helix, 48% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.71 | 0.77 | 71 | empty |
| 2 | 59 | 0.41 | 0.81 | 18 | empty |
| 3 | 68 | 0.40 | 0.80 | 17 | empty |
| 4 | 88 | 0.39 | 0.77 | 18 | empty |
| 5 | 63 | 0.38 | 0.79 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1861 Ų buried · 23 hydrogen bonds · protein-protein
- U–L · 684 Ų buried · 9 hydrogen bonds · protein-protein
- U–H · 509 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4DW2 · The crystal structure of uPA in complex with the Fab fragment of mAb-112 · the same entry in another collection · chain U against U, TM-score 1.00
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
- Elsewhere: RCSB PDB 4DW2 · PDBe 4DW2 · UniProt P00749
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