5VOF

DesGla-XaS195A Bound to Aptamer 11F7t and Rivaroxaban


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

DesGla-XaS195A Bound to Aptamer 11F7t and Rivaroxaban

Gunaratne, R.Kumar, S.Frederiksen, J.W.,Stayrook, S.Lohrmann, J.L.Perry, K.Chabata, C.V.Thalji, N.K.Ho, M.D.Arepally, G.Camire, R.M.Krishnaswamy, S.K.Sullenger, B.A.

(2018) Nat.Biotechnol. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor X
H
233Homo sapiensMutation(s): 1 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Go to Gene View: F10
Go to UniProtKB:  P00742
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor X
L
51Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Go to Gene View: F10
Go to UniProtKB:  P00742
Entity ID: 3
MoleculeChainsLengthOrganism
DNA/RNA (36-MER)A36synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RIV
Query on RIV

Download SDF File 
Download CCD File 
H
5-chloro-N-({(5S)-2-oxo-3-[4-(3-oxomorpholin-4-yl)phenyl]-1,3-oxazolidin-5-yl}methyl)thiophene-2-carboxamide
Rivaroxaban
C19 H18 Cl N3 O5 S
KGFYHTZWPPHNLQ-AWEZNQCLSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CFL
Query on CFL
A
DNA LINKINGC9 H13 F N3 O7 PDC
UFT
Query on UFT
A
DNA LINKINGC9 H12 F N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.220 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 55.744α = 90.00
b = 164.275β = 90.00
c = 124.521γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
REFMACphasing
Cootmodel building
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood InstituteUnited StatesHL-074124
National Institutes of Health/National Heart, Lung, and Blood InstituteUnited StatesHL-125422

Revision History 

  • Version 1.0: 2018-06-13
    Type: Initial release