4I7Y

Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II

Structural Biology Knowledgebase: 4I7Y SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.181

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4I7Y

Classification: HYDROLASE / HYDROLASE INHIBITOR / DNA

Total Structure Weight: 43060.68


Macromolecule Entities
Molecule Chains Length Organism Details
Prothrombin H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: HEAVY CHAIN (UNP Residues 364-622)
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Prothrombin L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: LIGHT CHAIN (UNP Residues 328-363)
Gene Name(s): F2 Gene View
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (27-MER) D 27 Synthetic construct HD22-27mer

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

H 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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

H SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000020 (DPN,AR7,0QE,PRO) H 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: 2.4 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.181
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 48.14 α = 90.00
b = 81.90 β = 99.66
c = 53.72 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-12-01
  • Released Date: 2013-10-16
  • Deposition author(s): Pica, A., Russo Krauss, I., Merlino, A., Mazzarella, L., Sica, F.

Revision History

  • 2014-01-01
    Type: Citation | Details: Citation update
  • 2013-12-11
    Type: Citation | Details: Citation update