3RXP

Crystal structure of Trypsin complexed with (1,5-dimethylpyrazol-3-yl)methanamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.196
  • R-Value Work: 0.168

Literature

Macromolecules
Sequence Display for 3RXP

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 23908.12

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 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SW3
Query on SW3

A 1-(1,5-dimethyl-1H-pyrazol-3-yl)methanamine
C6 H11 N3
JGYXJOBBROGMLL-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-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 %)
SW3 N/A in BindingDB
N/A in BindingMoad
IC50: 8300000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.196
  • R-Value Work: 0.168
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 54.45 α = 90.00
b = 58.34 β = 90.00
c = 66.65 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-05-10
  • Released Date: 2011-08-24
  • Deposition author(s): Yamane, J., Yao, M., Zhou, Y., Tanaka, I.

Revision History

  • Version 1_0: 2011-08-24

    Type: Initial release