1O38

Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors

Structural Biology Knowledgebase: 1O38 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.190

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1O38

Classification: hydrolase

Total Structure Weight: 23832.99

Macromolecule Entities
Molecule Chains Length Organism Details
BETA-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
653
Query on 653

A 5-(2-AMINOETHYL)-3-{5-[AMINO(IMINIO)METHYL]- 1H-BENZIMIDAZOL-2-YL}-1,1'-BIPHENYL-2-OLATE
CRA_23653 (Synonym)
C22 H22 N5 O
YYUZFCLHOQHMPT-UHFFFAOYSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
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 %)
653 N/A in BindingDB
Ki: 150 nM  BindingMOAD
Ki: 150 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.190
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 63.66 α = 90.00
b = 63.38 β = 90.00
c = 69.27 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-03-06
  • Released Date: 2003-09-02
  • Deposition author(s): Katz, B.A., Elrod, K., Verner, E., Mackman, R.L., Luong, C., Shrader, W.D., Sendzik, M., Spencer, J.R., Sprengeler, P.A., Kolesnikov, A., Tai, V.W., Hui, H.C., Breitenbucher, J.G., Allen, D., Janc, J.W.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4