3ATL

Crystal structure of trypsin complexed with benzamidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.188
  • R-Value Work: 0.159

Literature

Macromolecules
Sequence Display for 3ATL

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 23718.92

Macromolecule Entities
Molecule Chains Length Organism Details
Cationic trypsin A 223 Bos taurus EC#: 3.4.21.4 IUBMB
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: inferred by homology | Group: BETA-BARREL

Subgroup Name: Omp85-TpsB Outer Membrane Transporter Superfamily

Protein Name: BamABCDE complex of the Bam β-barrel assembly machine


Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BEN
Query on BEN

A BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

A DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BEN Ki: 31 - 39000 nM (100) BindingDB

N/A in BindingMoad
IC50: 17200 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.188
  • R-Value Work: 0.159
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 54.62 α = 90.00
b = 58.10 β = 90.00
c = 66.41 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-01-05
  • Released Date: 2011-08-24
  • Deposition author(s): Yamane, J., Yao, M., Tanaka, I.

Revision History

  • Version 1_0: 2011-08-24

    Type: Initial release