5WXR | pdb_00005wxr

Crystal structure of uPA in complex with upain-2-4-W3A

• PDB DOI: https://doi.org/10.2210/pdb5WXR/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, Phage display vector pTDisp
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2017-01-08 Released: 2018-07-11 
• Deposition Author(s): Jiang, L., Huang, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.234 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of uPA in complex with upain-2-4-W3A

Jiang, L., Huang, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 29.8 kDa 
• Atom Count: 2,131 
• Modeled Residue Count: 259 
• Deposited Residue Count: 267 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase-type plasminogen activator chain B	A [auth U]	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
upain-2-4-W3A peptide	B [auth P]	14	Phage display vector pTDisp	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.234 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.874	α = 90
b = 120.874	β = 90
c = 42.958	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-11 
Deposition Author(s): Jiang, L., Huang, M.

Revision History  

• Version 1.0: 2018-07-11
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary