8R7C

MutSbeta bound to compound CHDI-00915542 in the canonical DNA-mismatch bound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 
    0.231 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.205 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted YKWClick on this verticalbar to view details

This is version 1.0 of the entry. See complete history



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA mismatch repair protein Msh2
A, E
930Homo sapiensMutation(s): 0 
Gene Names: MSH2
UniProt & NIH Common Fund Data Resources
Find proteins for P43246 (Homo sapiens)
Explore P43246 
Go to UniProtKB:  P43246
PHAROS:  P43246
GTEx:  ENSG00000095002 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43246
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA mismatch repair protein Msh3
B, F
918Homo sapiensMutation(s): 0 
Gene Names: MSH3
UniProt & NIH Common Fund Data Resources
Find proteins for P20585 (Homo sapiens)
Explore P20585 
Go to UniProtKB:  P20585
PHAROS:  P20585
GTEx:  ENSG00000113318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20585
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
I [auth A],
O [auth E]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
YKW (Subject of Investigation/LOI)
Query on YKW

Download Ideal Coordinates CCD File 
K [auth B],
P [auth F]
~{N}-(4-chlorophenyl)-2-(4-ethylpiperazin-1-yl)pteridin-4-amine
C18 H20 Cl N7
BZUWWBFNILEVHG-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
J [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
M [auth B],
N [auth B],
Q [auth F],
S [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
L [auth B],
R [auth F],
T [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free:  0.231 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.205 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.222α = 110.029
b = 104.789β = 91.198
c = 121.263γ = 110.501
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted YKWClick on this verticalbar to view details

Entry History & Funding Information

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release