2ZQ2

Exploring trypsin S3 pocket

Structural Biology Knowledgebase: 2ZQ2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.162
  • R-Value Work: 0.116

Literature

Macromolecules
Sequence Display for 2ZQ2

Classification: Hydrolase / Hydrolase Inhibitor

Total Structure Weight: 24146.42

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

Membrane Protein

Source: inferred by homology | Group: BETA-BARREL

Subgroup Name: Omp85-TpsB Outer Membrane Transporter Superfamily

Protein Name: BamABCDE complex of the Bam β-barrel assembly machine


Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
13U
Query on 13U

A N-cyclooctylglycyl-N-(4-carbamimidoylbenzyl)- L-prolinamide
(2S)-N-[(4-carbamimidoylphenyl)methyl]-1- [2-(cyclooctylamino)ethanoyl]pyrrolidine- 2-carboxamide (Synonym)
C23 H35 N5 O2
MMLOIDMSBRJZAE-FQEVSTJZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
13U N/A in BindingDB
Kd: 276 nM  BindingMOAD
Kd: 276 nM  PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000589
Query on PRD_000589
A N-cyclooctylglycyl-N-(4-carbamimidoylbenzyl)-L-prolinamide Peptide-like /
Thrombin Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.162
  • R-Value Work: 0.116
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 61.40 α = 90.00
b = 63.90 β = 90.00
c = 69.70 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-08-03
  • Released Date: 2009-08-04
  • Deposition author(s): Brandt, T., Baum, B., Heine, A., Klebe, G.

Revision History

  • 2014-01-22
    Type: Citation | Details: Citation update
  • 2013-02-27
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update