2ZHD

Exploring trypsin S3 pocket

Structural Biology Knowledgebase: 2ZHD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.162

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2ZHD

Classification: Hydrolase / Hydrolase Inhibitor

Total Structure Weight: 24136.36

Macromolecule Entities
Molecule Chains Length Organism Details
Cationic trypsin A 223 Bos taurus EC#: 3.4.21.4 IUBMB
Gene Name(s):

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
12U
Query on 12U

A N-cycloheptylglycyl-N-(4-carbamimidoylbenzyl)- L-prolinamide
(2S)-N-[(4-carbamimidoylphenyl)methyl]-1- [2-(cycloheptylamino)ethanoyl]pyrrolidine- 2-carboxamide (Synonym)
C22 H33 N5 O2
BYTJPDBCLWUEBU-IBGZPJMESA-N
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)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
12U N/A in BindingDB
N/A in BindingMoad
Kd: 287 nM  PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000588 (00S,PRO,CGH) A N-cycloheptylglycyl-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: 1.94 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.162
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 61.00 α = 90.00
b = 63.60 β = 90.00
c = 69.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-02-04
  • Released Date: 2009-02-10
  • 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: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4