Research workbench
The catalytic domain of murine urokinase-type plasminogen activator in complex with the active site binding inhibitory nanobody NB22
Analyse The catalytic domain of murine urokinase-type plasminogen activator in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LHR
- Type
- protein
- Length
- 361 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urokinase-type plasminogen activator; Camelid-derived antibody fragment NB22
- EC
- 3.4.21.73
- UniProt
- P06869
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 245 | 10% helix, 40% strand | P06869 |
| B | Camelid-derived antibody fragment NB22 | protein | 116 | 5% helix, 48% strand | — |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.50 | 0.75 | 46 | empty |
| 2 | 56 | 0.38 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 915 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5LHR · The catalytic domain of murine urokinase-type plasminogen activator in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
- P06869 · AlphaFold monomer V2.0 prediction for urokinase-type plasminogen activator (P06869) · a predicted model of the same protein · chain A 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 P06869
- Elsewhere: RCSB PDB 5LHR · PDBe 5LHR · UniProt P06869
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