MolNFT v1 · #125731 · protein
The egr-cmk active site inhibited catalytic domain of murine urokinase-type plasminogen activator in complex with the allosteric inhibitory nanobody NB7
5LHQ: “The egr-cmk active site inhibited catalytic domain of murine urokinase-type plasminogen activator in complex…”. X-ray diffraction, 2 ligands (0GJ, SO4), 3 pockets (best druggability 0.56). MolNFT v1 #125731 on GenesisL1: 3D…
- PDB
- 5LHQ
- 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 NB7
- EC
- 3.4.21.73
- UniProt
- P06869
- Ligands
- 0GJ, SO4
- Pockets
- 3 · best druggability 0.56
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, 36% strand | P06869 |
| B | Camelid-derived antibody fragment NB7 | protein | 135 | 10% helix, 44% strand | — |
Ligands and binding sites
- 0GJ · L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide · ligand · chains A
- SO4 · Sulfate ion · ion · 11 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 | 56 | 0.56 | 0.89 | 15 | empty |
| 2 | 119 | 0.46 | 0.79 | 25 | 0GJ |
| 3 | 73 | 0.33 | 0.75 | 19 | SO4 |
Interfaces
1 interface between chains.
- A–B · 969 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 5LHQ · The EGR-cmk active site inhibited catalytic domain of murine urokinase-type plasminogen… · 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 5LHQ · PDBe 5LHQ · UniProt P06869
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