1Z8I

Crystal structure of the thrombin mutant G193A bound to PPACK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.199

Literature

Macromolecules
Sequence Display for 1Z8I

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 35223.02

Macromolecule Entities
Molecule Chains Length Organism Details
Thrombin light chain A 39 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: sequence database residues 324-361
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Thrombin heavy chain B 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: sequence database residues 364-622
Mutation: G193A
Gene Name(s): F2 Gene View

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0G6
Query on 0G6

B D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}- 1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide
PPACK (Synonym)
C21 H34 Cl N6 O3
DVFLYEYCMMLBTQ-VSZNYVQBSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000020
Query on PRD_000020
B D-Phe-Pro-Arg-CH2Cl Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.199
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 49.82 α = 90.00
b = 73.65 β = 90.00
c = 89.77 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-03-30
  • Released Date: 2005-05-17
  • Deposition author(s): Bobofchak, K.M., Pineda, A.O., Mathews, F.S., Di Cera, E.

Revision History

  • 2008-04-30
    Type: Version format compliance
  • 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • 2013-02-27
    Type: Other