3M61 | pdb_00003m61

Crystal structure of complex of urokinase and a upain-1 variant(W3A) in pH4.6 condition

• PDB DOI: https://doi.org/10.2210/pdb3M61/pdb

• Classification: Hydrolase/Hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2010-03-15 Released: 2010-04-07 
• Deposition Author(s): Jiang, L., Yuan, C., Wind, T., Andreasen, P.A., Chen, L., Meehan, E.J., Huang, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.243 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of complex of urokinase and a upain-1 variant(W3A) in pH4.6 condition

Jiang, L., Yuan, C., Wind, T., Andreasen, P.A., Chen, L., Meehan, E.J., 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: 29.82 kDa 
• Atom Count: 2,190 
• Modeled Residue Count: 259 
• Deposited Residue Count: 265 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase-type plasminogen activator	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-1 W3A	B [auth P]	12	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.243 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.705	α = 90
b = 121.705	β = 90
c = 43.128	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-07 
Deposition Author(s): Jiang, L., Yuan, C., Wind, T., Andreasen, P.A., Chen, L., Meehan, E.J., Huang, M.

Revision History  

• Version 1.0: 2010-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary