3I78

35/99/170/186/220-loops of FXa in SGT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Combinatorial Enzyme Design Probes Allostery and Cooperativity in the Trypsin Fold.

Page, M.J.Di Cera, E.

(2010) J.Mol.Biol. 399: 306-319

  • DOI: 10.1016/j.jmb.2010.04.024
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Converting one enzyme into another is challenging due to the uneven distribution of important amino acids for function in both protein sequence and structure. We report a strategy for protein engineering allowing an organized mixing and matching of g ...

    Converting one enzyme into another is challenging due to the uneven distribution of important amino acids for function in both protein sequence and structure. We report a strategy for protein engineering allowing an organized mixing and matching of genetic material that leverages lower throughput with increased quality of screens. Our approach successfully tested the contribution of each surface-exposed loop in the trypsin fold alone and the cooperativity of their combinations towards building the substrate selectivity and Na(+)-dependent allosteric activation of the protease domain of human coagulation factor Xa into a bacterial trypsin. As the created proteases lack additional protein domains and protein co-factor activation mechanism requisite for the complexity of blood coagulation, they are stepping-stones towards further understanding and engineering of artificial clotting factors.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Trypsin
A
229Streptomyces griseusMutation(s): 0 
Gene Names: sprT
EC: 3.4.21.4
Find proteins for P00775 (Streptomyces griseus)
Go to UniProtKB:  P00775
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BEN
Query on BEN

Download SDF File 
Download CCD File 
A
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.208 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 113.710α = 90.00
b = 113.710β = 90.00
c = 52.616γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data collection
PDB_EXTRACTdata extraction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance