6OQ3

Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.244 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Inhibition of the HEG1-KRIT1 interaction increases KLF4 and KLF2 expression in endothelial cells

Lopez-Ramirez, M.A.McCurdy, S.Li, W.Haynes, M.K.Hale, P.Francisco, K.Oukoloff, K.Bautista, M.Choi, C.H.Sun, H.Gongol, B.Shyy, J.Y.Ballatore, C.Sklar, L.A.Gingras, A.R.

(2021) FASEB Bioadv 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Krev interaction trapped protein 1A322Homo sapiensMutation(s): 0 
Gene Names: KRIT1CCM1
UniProt & NIH Common Fund Data Resources
Find proteins for O00522 (Homo sapiens)
Explore O00522 
Go to UniProtKB:  O00522
PHAROS:  O00522
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related protein Rap-1bB167Homo sapiensMutation(s): 0 
Gene Names: RAP1BOK/SW-cl.11
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P61224 (Homo sapiens)
Explore P61224 
Go to UniProtKB:  P61224
PHAROS:  P61224
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP (Subject of Investigation/LOI)
Query on GNP

Download Ideal Coordinates CCD File 
E [auth B]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
7WO (Subject of Investigation/LOI)
Query on 7WO

Download Ideal Coordinates CCD File 
C [auth A]2-hydroxynaphthalene-1-carbaldehyde
C11 H8 O2
NTCCNERMXRIPTR-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.244 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.11α = 90
b = 76.83β = 92.281
c = 58.21γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2019-04-25 
  • Released Date: 2020-06-24 
  • Deposition Author(s): Gingras, A.R.

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2021-03-31
    Changes: Database references, Derived calculations