MolNFT v1 · #96454 · protein
Human urokinase-type plasminogen activator (upa) in complex with a bicyclic peptide inhibitor (UK18-D-aba)
4JK6: “Human urokinase-type plasminogen activator (upa) in complex with a bicyclic peptide inhibitor (UK18-D-aba)”. X-ray diffraction, 4 ligands (ZBR, SO4, NH2), 1 pocket (best druggability 0.34). MolNFT v1 #96454 on GenesisL1: 3D…
- PDB
- 4JK6
- Type
- protein
- Length
- 262 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urokinase-type plasminogen activator; Bicyclic peptide UK18-D-aba inhibitor of upa
- EC
- 3.4.21.73
- UniProt
- P00749
- Ligands
- ZBR, SO4, NH2, CL
- Pockets
- 1 · best druggability 0.34
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 245 | 11% helix, 39% strand | P00749 |
| B | Bicyclic peptide UK18-D-aba inhibitor of upa | protein | 17 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZBR · 1,3,5-tris(bromomethyl)benzene · ligand · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- NH2 · Amino group · ion · chains B
- CL · Chloride ion · ion · chains A
- P6G · Hexaethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.34 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 790 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 3 covalent, 1 modified (disulfide, covalent ligand, nonstandard).
Compared structures
- 4JK6 · Human urokinase-type Plasminogen Activator (uPA) in complex with a bicyclic peptide… · the same entry in another collection · chain A against A, 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 4JK6 · PDBe 4JK6 · UniProt P00749
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