3RXJ

Crystal structure of Trypsin complexed with 4-guanidinobenzoic acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history. 


Literature

In-crystal affinity ranking of fragment hit compounds reveals a relationship with their inhibitory activities

Yamane, J., Yao, M., Zhou, Y., Hiramatsu, Y., Fujiwara, K., Yamaguchi, T., Yamaguchi, H., Togame, H., Tsujishita, H., Takemoto, H., Tanaka, I.

(2011) J Appl Crystallogr 44: 798-804


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cationic trypsin223Bos taurusMutation(s): 0 
EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00760
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GBS
Query on GBS
Download Ideal Coordinates CCD File 
J [auth A]4-carbamimidamidobenzoic acid
C8 H9 N3 O2
SXTSBZBQQRIYCU-UHFFFAOYSA-N
GOL
Query on GOL
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A]		DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
GBS PDBBind:  3RXJ IC50: 8.73e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.393α = 90
b = 58.393β = 90
c = 66.551γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 2.0: 2023-11-01
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2024-11-13
    Changes: Structure summary