3KGP

Crystal Structures of Urokinase-type Plasminogen Activator in Complex with 4-(Aminomethyl) Benzoic Acid and 4-(Aminomethyl-phenyl)-methanol

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

Crystal Structures of Urokinase-type Plasminogen Activator in Complex with 4-(Aminomethyl) Benzoic Acid and 4-(Aminomethyl-phenyl)-methanol

Jiang, L.-G., Zhao, G.-X., Bian, X.-B., Yuan, C., Huang, Z.-X., Huang, M.-D.

(2009) Chin J Struct Chem 28: 253-259


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Urokinase-type plasminogen activator253Homo sapiensMutation(s): 2 
Gene Names: PLAU
EC: 3.4.21.73
UniProt & NIH Common Fund Data Resources
Find proteins for P00749 (Homo sapiens)
Explore P00749 
Go to UniProtKB:  P00749
PHAROS:  P00749
GTEx:  ENSG00000122861 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00749
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4AZ
Query on 4AZ
Download Ideal Coordinates CCD File 
B [auth A]4-(aminomethyl)benzoic acid
C8 H9 N O2
QCTBMLYLENLHLA-UHFFFAOYSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
4AZ PDBBind:  3KGP Ki: 2.68e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.834α = 90
b = 120.834β = 90
c = 42.488γ = 120
Software Package:
Software NamePurpose
CNSrefinement
PROTEUM PLUSdata collection
PROTEUM PLUSdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-12-25
    Changes: Data collection
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description