Research workbench
Human urokinase-type plasminogen activator (upa) in complex with a bicyclic peptide inhibitor (UK18-D-ser)
Analyse Human urokinase-type plasminogen activator (upa) in complex with a bicyclic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JK5
- 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-ser, upa inhibitor
- EC
- 3.4.21.73
- UniProt
- P00749
- Ligands
- ZBR, SO4, CL, NH2
- Pockets
- 2 · best druggability 0.54
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-ser, upa inhibitor | 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
- CL · Chloride ion · ion · 2 copies · chains A, B
- NH2 · Amino group · ion · chains B
- P6G · Hexaethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 59 | 0.54 | 0.88 | 21 | empty |
| 2 | 65 | 0.38 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 810 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 3 covalent, 1 d-amino (disulfide, covalent ligand, D-amino acid).
Compared structures
- 4JK5 · 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 4JK5 · PDBe 4JK5 · UniProt P00749
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