1V2S

Benzamidine in complex with bovine trypsin variant X(SSFI.Glu)bT.D1

Structural Biology Knowledgebase: 1V2S SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.197

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1V2S

Classification: HYDROLASE

Total Structure Weight: 23707.85

Macromolecule Entities
Molecule Chains Length Organism Details
Trypsin T 223 Bos taurus EC#: 3.4.21.4 IUBMB
Mutation: Y172S, P173S, G174F, Q175I, S217E
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 (97) BindingDB

Ki: 68000 nM  BindingMOAD
Ki: 68000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.197
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 54.58 α = 90.00
b = 54.58 β = 90.00
c = 136.62 γ = 120.00

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