4XSK | pdb_00004xsk

Structure of PAItrap, an uPA mutant

• PDB DOI: https://doi.org/10.2210/pdb4XSK/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Komagataella phaffii GS115
• Mutation(s): Yes 


• Deposited: 2015-01-22 Released: 2016-02-03 
• Deposition Author(s): Gong, L., Proulle, V., Hong, Z., Lin, Z., Liu, M., Yuan, C., Lin, L., Furie, B., Flaumenhaft, R., Andreasen, P., Furie, B., Huang, M.
• Funding Organization(s): National Natural Science Foundation of China, NFSC, National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), CAS/SFEA International Partnership Program for Creative Research Teams, NSF of Fujian Province

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.209 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Structure of PAItrap, an uPA mutant

Gong, L., Proulle, V., Hong, Z., Lin, Z., Liu, M., Yuan, C., Lin, L., Furie, B., Flaumenhaft, R., Andreasen, P., Furie, B., Huang, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.43 kDa 
• Atom Count: 2,108 
• Modeled Residue Count: 246 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase-type plasminogen activator	A [auth U]	246	Homo sapiens	Mutation(s): 5  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 U], E [auth U]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4	B [auth U], C [auth U]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth U], G [auth U]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.209 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.025	α = 90
b = 121.025	β = 90
c = 42.774	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-02-03 
Deposition Author(s): Gong, L., Proulle, V., Hong, Z., Lin, Z., Liu, M., Yuan, C., Lin, L., Furie, B., Flaumenhaft, R., Andreasen, P., Furie, B., Huang, M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31161130356
NFSC	China	31370737
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL087203
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL095084
CAS/SFEA International Partnership Program for Creative Research Teams	China	--
NSF of Fujian Province	China	2012J05071

Revision History  

• Version 1.0: 2016-02-03
  Type: Initial release
  
• Version 1.1: 2017-10-18
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2022-03-23
  Changes: Author supporting evidence, Database references
• Version 1.3: 2023-11-08
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary