MolNFT v1 · #125730 · protein
The P-aminobenzamidine active site inhibited catalytic domain of murine urokinase-type plasminogen activator in complex with the allosteric inhibitory nanobody NB7
5LHP: “The P-aminobenzamidine active site inhibited catalytic domain of murine urokinase-type plasminogen activator…”. X-ray diffraction, 2 ligands (PBZ, SO4), 3 pockets (best druggability 0.55). MolNFT v1 #125730 on GenesisL1: 3D…
- PDB
- 5LHP
- Type
- protein
- Length
- 382 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urokinase-type plasminogen activator; Camelid-derived antibody fragment
- EC
- 3.4.21.73
- UniProt
- P06869
- Ligands
- PBZ, SO4
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 247 | 11% helix, 35% strand | P06869 |
| B | Camelid-derived antibody fragment | protein | 135 | 10% helix, 44% strand | — |
Ligands and binding sites
- PBZ · P-amino benzamidine · ligand · chains A
- SO4 · Sulfate ion · ion · 14 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
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 | 60 | 0.55 | 0.88 | 16 | empty |
| 2 | 141 | 0.45 | 0.76 | 27 | SO4, PBZ |
| 3 | 82 | 0.34 | 0.75 | 19 | SO4 |
Interfaces
1 interface between chains.
- A–B · 948 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 5LHP · The p-aminobenzamidine active site inhibited catalytic domain of murine urokinase-type… · 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 5LHP · PDBe 5LHP · UniProt P06869
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