1DLK

CRYSTAL STRUCTURE ANALYSIS OF DELTA-CHYMOTRYPSIN BOUND TO A PEPTIDYL CHLOROMETHYL KETONE INHIBITOR

Structural Biology Knowledgebase: 1DLK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.207

Literature

Macromolecules
Sequence Display for 1DLK

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 51888.05

Macromolecule Entities
Molecule Chains Length Organism Details
Thrombin light chain A, C 13 Bos taurus EC#: 3.4.21.1 IUBMB
Fragment: RESIDUES 1-13
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Thrombin heavy chain B, D 230 Bos taurus EC#: 3.4.21.1 IUBMB
Fragment: RESIDUES 16-245
Gene Name(s):
peptidic inhibitor E, F 5 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CL
Query on CL

B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 3 Unique
ID Chains Type Formula 2D Diagram Parent
PHQ
Query on PHQ
E, F NON-POLYMER C8 H7 Cl O2 --
HPH
Query on HPH
E, F peptide-like C9 H13 N O2 PHE
0QE
Query on 0QE
E, F NON-POLYMER C H3 Cl --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.207
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 121.17 α = 90.00
b = 121.17 β = 90.00
c = 116.08 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-12-10
  • Released Date: 2000-05-03
  • Deposition author(s): Mac Sweeney, A., Birrane, G., Walsh, M.A., O'Connell, T., Malthouse, J.P.G.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description