6EO7

X-ray structure of the complex between human alpha-thrombin and modified 15-mer DNA aptamer containing 5-(3-(acetamide-N-yl)-1-propen-1-yl)-2'-deoxyuridine residue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.161

Literature

Macromolecules
Sequence Display for 6EO7

Classification: HYDROLASE / DNA

Total Structure Weight: 39440.18


Macromolecule Entities
Molecule Chains Length Organism Details
Prothrombin L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Prothrombin H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Macromolecule Entities
Molecule Chains Length Organism Details
GA68B2 - MODIFIED HUMAN THROMBIN BINDING APTAMER D 15 Unidentified THROMBIN-SPECIFIC 15-MER DNA APTAMER CONTAINING 5-(3-(ACETAMIDE-N-YL)-1-PROPEN-1-YL)-2'-DEOXYURIDINE RESIDUE

Small Molecules
Ligands 4 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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

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

H SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
8DT
Query on 8DT
D DNA linking C14 H20 N3 O9 P DU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.161
  • Space Group: P 32 2 1

Unit Cell:

Length (Å) Angle (°)
a = 94.58 α = 90.00
b = 94.58 β = 90.00
c = 125.57 γ = 120.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2017-10-09
  • Released Date: 2017-10-18
  • Deposition author(s): Dolot, R.M., Nawrot, B., Yang, X.
  • This entry supercedes: 5LUY

Revision History

  • Version 1_0: 2017-10-18

    Type: Initial release