1V2J

BENZAMIDINE IN COMPLEX WITH BOVINE TRYPSIN VARIANT X(SSRI)bT.C1

Structural Biology Knowledgebase: 1V2J SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.216

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1V2J

Classification: HYDROLASE

Total Structure Weight: 23579.73

Macromolecule Entities
Molecule Chains Length Organism Details
Trypsin T 223 Bos taurus EC#: 3.4.21.4 IUBMB
Mutation: Y172S, P173S, G174R, Q175I
Gene Name(s):

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

T BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

T SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

T CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BEN Ki: 31 - 39000 nM (98) BindingDB

Ki: 566000 nM  BindingMOAD
Ki: 566000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.216
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 61.10 α = 90.00
b = 70.34 β = 90.00
c = 64.15 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-10-17
  • Released Date: 2004-06-01
  • Deposition author(s): Rauh, D., Klebe, G., Stubbs, M.T.

Revision History

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