6EO6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.168
  • R-Value Work: 0.145

Literature

Macromolecules
Sequence Display for 6EO6

Classification: Hydrolase / DNA

Total Structure Weight: 39555.31


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
GA63A - TBA MODIFIED APTAMER D 15 Unidentified 15-MER DNA APTAMER SPECIFIC TO HUMAN ALPHA-THROMBIN, CONTAINING 5-(3-(2-(1H-INDOL-3-YL)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
77Y
Query on 77Y
D DNA linking C22 H25 N4 O9 P DU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.168
  • R-Value Work: 0.145
  • Space Group: P 32 2 1

Unit Cell:

Length (Å) Angle (°)
a = 94.10 α = 90.00
b = 94.10 β = 90.00
c = 124.71 γ = 120.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2017-10-09
  • Released Date: 2017-10-25
  • Deposition author(s): Dolot, R.M., Nawrot, B., Yang, X.
  • This entry supercedes: 5LUW

Revision History

  • Version 1_0: 2017-10-25

    Type: Initial release