MolNFT v1 · #125728 · protein
The catalytic domain of murine urokinase-type plasminogen activator in complex with the allosteric inhibitory nanobody NB7
5LHN: “The catalytic domain of murine urokinase-type plasminogen activator in complex with the allosteric inhibitory…”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.54). MolNFT v1 #125728 on GenesisL1: 3D structure…
- PDB
- 5LHN
- Type
- protein
- Length
- 373 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urokinase-type plasminogen activator; Camelid-derived antibody fragment NB7
- EC
- 3.4.21.73
- UniProt
- P06869
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 238 | 12% helix, 37% strand | P06869 |
| B | Camelid-derived antibody fragment NB7 | protein | 135 | 10% helix, 44% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.54 | 0.86 | 16 | empty |
| 2 | 69 | 0.36 | 0.78 | 21 | empty |
| 3 | 64 | 0.32 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 939 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 5LHN · 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 0.96
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 5LHN · PDBe 5LHN · UniProt P06869
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