3KHV

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

• PDB DOI: https://doi.org/10.2210/pdb3KHV/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2009-10-30 Released: 2009-12-01 
• Deposition Author(s): Jiang, L.-G., Zhao, G.-X., Bian, X.-B., Yuan, C., Huang, Z.-X., Huang, M.-D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.293 
• R-Value Work: 0.228 
• R-Value Observed: 0.228 

Starting Model: experimental

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.83 kDa 
• Atom Count: 2,175 
• Modelled Residue Count: 239 
• Deposited Residue Count: 253 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase-type plasminogen activator	A	253	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	D [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
4AL	B [auth A]	[4-(aminomethyl)phenyl]methanol C8 H11 N O WMOUKOAUAFESMR-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
4AL	PDBBind:  3KHV	Ki: 1.40e+7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.293 
• R-Value Work: 0.228 
• R-Value Observed: 0.228 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.826	α = 90
b = 120.826	β = 90
c = 42.355	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PROTEUM PLUS	data collection
PROTEUM PLUS	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-01 
Deposition Author(s): Jiang, L.-G., Zhao, G.-X., Bian, X.-B., Yuan, C., Huang, Z.-X., Huang, M.-D.

Revision History  

• 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
• Version 1.5: 2024-10-30
  Changes: Structure summary