2ZFT

Exploring trypsin S3 pocket


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.154

Literature

Macromolecules
Sequence Display for 2ZFT

Classification: Hydrolase / Hydrolase Inhibitor

Total Structure Weight: 24182.35

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 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
10U
Query on 10U

A (S)-N-(4-carbamimidoylbenzyl)-1-(2-(cyclopentylamino)ethanoyl)pyrrolidine- 2-carboxamide
(2S)-1-[cyclopentylamino)acetyl-N-{4-[amino(imino)methyl]benzyl}pyrrolidine- 2-carboxamide (Synonym)
C20 H29 N5 O2
WXYKSWZWRHMJTE-KRWDZBQOSA-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)
DMS
Query on DMS

A DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-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 %)
10U N/A in BindingDB
N/A in BindingMoad
Kd: 300 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.154
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 54.60 α = 90.00
b = 54.60 β = 90.00
c = 108.50 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-01-11
  • Released Date: 2009-01-13
  • Deposition author(s): Brandt, T., Baum, B., Heine, A., Klebe, G.

Revision History

  • Version 1_0: 2009-01-13

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Non-polymer description, Version format compliance

  • Version 1_2: 2013-02-27

    Type: Other

  • Version 1_3: 2014-01-22

    Type: Database references