4JK5

Human urokinase-type Plasminogen Activator (uPA) in complex with a bicyclic peptide inhibitor (UK18-D-Ser)

Structural Biology Knowledgebase: 4JK5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.142

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4JK5

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 30501.98

Macromolecule Entities
Molecule Chains Length Organism Details
Urokinase-type plasminogen activator A 245 Homo sapiens EC#: 3.4.21.73 IUBMB
Fragment: Catalytic domain
Mutation: C122A, N145Q
Gene Name(s): PLAU Gene View
bicyclic peptide UK18-D-Ser, uPA inhibitor B 18 Synthetic construct

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZBR
Query on ZBR

B 1,3,5-tris(bromomethyl)benzene
C9 H9 Br3
GHITVUOBZBZMND-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
P6G
Query on P6G

A HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400 (Synonym)
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000926 (SER,VAL,TYR,DSN,ALA,ARG,ASP,CYS,GLU,NH2,GLY) B bicyclic peptide UK18-D-Ser Cyclic peptide /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.142
  • Space Group: H 3

Unit Cell:

Length (Å) Angle (°)
a = 121.24 α = 90.00
b = 121.24 β = 90.00
c = 42.63 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-03-09
  • Released Date: 2013-07-17
  • Deposition author(s): Buth, S.A., Leiman, P.G., Chen, S., Heinis, C.

Revision History

  • 2013-07-31
    Type: Citation | Details: Citation update