6OQ4 | pdb_00006oq4

Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.264 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.231 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6OQ4

Ligand Structure Quality Assessment 


This is version 1.2 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 

Macromolecule Content 

  • Total Structure Weight: 57.33 kDa 
  • Atom Count: 4,047 
  • Modeled Residue Count: 474 
  • Deposited Residue Count: 489 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Krev interaction trapped protein 1322Homo sapiensMutation(s): 0 
Gene Names: KRIT1, CCM1
UniProt & NIH Common Fund Data Resources
Find proteins for O00522 (Homo sapiens)
Explore O00522 
Go to UniProtKB:  O00522
PHAROS:  O00522
GTEx:  ENSG00000001631 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00522
Sequence Annotations
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ras-related protein Rap-1b167Homo sapiensMutation(s): 0 
Gene Names: RAP1B, OK/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
GTEx:  ENSG00000127314 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61224
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP

Query on GNP


Download:Ideal Coordinates CCD File
E [auth B]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
N0G
(Subject of Investigation/LOI)

Query on N0G


Download:Ideal Coordinates CCD File
C [auth A]2-{(Z)-[(2-hydroxynaphthalen-1-yl)methylidene]amino}-N-[(1S)-1-phenylethyl]benzamide
C26 H22 N2 O2
UXJFDYIHRJGPFS-PTXYPZRJSA-N
MG

Query on MG


Download:Ideal Coordinates CCD File
D [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.264 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.231 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.35α = 90
b = 77.41β = 91.64
c = 58.62γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references