4JK6

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

Structural Biology Knowledgebase: 4JK6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.153

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4JK6

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 30464.56

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-Aba inhibitor of uPA B 18 Synthetic construct

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

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
JSmol
P6G
Query on P6G

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

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
JSmol
ZBR
Query on ZBR

B 1,3,5-tris(bromomethyl)benzene
C9 H9 Br3
GHITVUOBZBZMND-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000927 B bicyclic peptide UK18-D-Aba inhibitor of uPA Cyclic peptide /
Inhibitor
Ligand Explorer

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.153
  • Space Group: H 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 121.22 α = 90.00
b = 121.22 β = 90.00
c = 42.73 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