5YC7

The crystal structure of uPA in complex with 4-Bromobenzylamirne at pH7.4

• PDB DOI: https://doi.org/10.2210/pdb5YC7/pdb
• Entry: 5YC7 supersedes: 4JNL

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2017-09-06 Released: 2018-10-03 
• Deposition Author(s): Jiang, L.G., Zhang, X., Huang, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.262 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Halogen bonding for the design of inhibitors by targeting the S1 pocket of serine proteases

Jiang, L.G., Zhang, X., Zhou, Y., Chen, Y.Y., Luo, Z.P., Li, J.Y., Yuan, C., Huang, M.D.

(2018) RSC Adv 8: 28189-28197

• DOI: https://doi.org/10.1039/c8ra03145b

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 28 kDa 
• Atom Count: 1,995 
• Modelled 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): 0  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PZH	B [auth U]	1-(4-BROMOPHENYL)METHANAMINE C7 H8 Br N XRNVSPDQTPVECU-UHFFFAOYSA-N
SO4	C [auth U]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.262 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.575	α = 90
b = 121.575	β = 90
c = 42.212	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-03 
Deposition Author(s): Jiang, L.G., Zhang, X., Huang, M.D.
• This entry supersedes: 4JNL

Revision History  

• Version 1.0: 2018-10-03
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary