1YP9

Trypsin Inhibitor Complex

Structural Biology Knowledgebase: 1YP9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.174

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YP9

Classification: HYDROLASE

Total Structure Weight: 24057.29

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

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

A (1R,3AS,4R,8AS,8BR)-4-(2-BENZO[1,3]DIOXOL- 5-YLMETHYL)-1-BENZYL-3-OXO-DECAHYDRO-PYRROLO[3,4- A]PYRROZILIN-4-YL-BENZAMIDINE
C31 H32 N4 O3
APELQVQIJUTSME-UDOPOUDQSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
UIZ N/A in BindingDB
Ki: 7700 nM  BindingMOAD
Ki: 7700 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.174
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 61.20 α = 90.00
b = 63.50 β = 90.00
c = 69.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-01-31
  • Released Date: 2006-01-17
  • Deposition author(s): Fokkens, J., Obst-Sander, U., Heine, A., Diederich, F., Klebe, G.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4