1C2D

RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES

Structural Biology Knowledgebase: 1C2D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.193

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1C2D

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 23867.91

Macromolecule Entities
Molecule Chains Length Organism Details
TRYPSIN A 223 Bos taurus EC#: 3.4.21.4 IUBMB
Details: COMPLEXED WITH BIS(5-AMIDINO-2-BENZIMIDAZOLYL)METHANE KETONE
Gene Name(s):

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BAK
Query on BAK

A BIS(5-AMIDINO-2-BENZIMIDAZOLYL)METHANE KETONE
C17 H16 N8 O
VVVXDHROXQUONB-UHFFFAOYSA-P
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-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)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BAK N/A in BindingDB
Ki: 5.2 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.193
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 54.94 α = 90.00
b = 54.94 β = 90.00
c = 109.75 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-07-21
  • Released Date: 2000-07-26
  • Deposition author(s): Katz, B.A., Luong, C.

Revision History

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