4DII

X-ray structure of the complex between human alpha thrombin and thrombin binding aptamer in the presence of potassium ions

Structural Biology Knowledgebase: 4DII SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.174

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DII

Classification: HYDROLASE / HYDROLASE INHIBITOR / DNA

Total Structure Weight: 39559.04


Macromolecule Entities
Molecule Chains Length Organism Details
Prothrombin L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: Light chain (UNP Residues 328-363)
Gene Name(s): F2 Gene View
Prothrombin H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: Heavy chain (UNP Residues 364-622)
Gene Name(s): F2 Gene View
Macromolecule Entities
Molecule Chains Length Organism Details
Thrombin binding aptamer D 15 Synthetic construct

Small Molecules
Ligands 6 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

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

H, L ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

D POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

H CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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: 2.05 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.174
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 43.37 α = 68.97
b = 45.30 β = 86.11
c = 51.52 γ = 69.66

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-01-31
  • Released Date: 2012-07-18
  • Deposition author(s): Russo Krauss, I., Merlino, A., Mazzarella, L., Sica, F.

Revision History

  • 2013-02-27
    Type: Other | Details: Add PRD info
  • 2012-09-26
    Type: Citation | Details: Citation update