3MWI | pdb_00003mwi

The complex crystal Structure of Urokianse and 5-nitro-1H-indole-2-amidine

• PDB DOI: https://doi.org/10.2210/pdb3MWI/pdb

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


• Deposited: 2010-05-06 Released: 2011-06-01 
• Deposition Author(s): Jiang, L.G., Yu, H.Y., Yuan, C., Huang, Z.X., Huang, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 
  0.297 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

The complex crystal Structure of Urokianse and 5-nitro-1H-indole-2-amidine

Jiang, L.G., Yu, H.Y., Yuan, C., Huang, Z.X., Huang, M.D.

To be published.

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: 28.1 kDa 
• Atom Count: 2,115 
• 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): 1  Gene Names: Human 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
B25	B [auth U]	5-nitro-1H-indole-2-carboximidamide C9 H8 N4 O2 ZFLOQYGDSBVASK-UHFFFAOYSA-N
SO4	C [auth U], D [auth U]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free:  0.297 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.465	α = 90
b = 121.465	β = 90
c = 43.097	γ = 120

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
AMoRE	phasing
REFMAC	refinement
SAINT	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-01 
Deposition Author(s): Jiang, L.G., Yu, H.Y., Yuan, C., Huang, Z.X., Huang, M.D.

Revision History  

• Version 1.0: 2011-06-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-12-25
  Changes: Data collection, Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary