9FMR

Structure of DDB1/Cdk12/Cyclin K with molecular glue SR-4835


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 
    0.250 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Models: experimental
View more details

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 RMFClick on this verticalbar to view details

This is version 1.0 of the entry. See complete history


Literature

Structure of DDB1/Cdk12/Cyclin K with molecular glue SR-4835

Anand, K.Schmitz, M.Geyer, M.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage-binding protein 1
A, D, G
864Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens)
Explore Q16531 
Go to UniProtKB:  Q16531
PHAROS:  Q16531
GTEx:  ENSG00000167986 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16531
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 12
B, E, H
351Homo sapiensMutation(s): 0 
Gene Names: CDK12CRK7CRKRSKIAA0904
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYV4 (Homo sapiens)
Explore Q9NYV4 
Go to UniProtKB:  Q9NYV4
PHAROS:  Q9NYV4
GTEx:  ENSG00000167258 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NYV4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-K
C, F, I
268Homo sapiensMutation(s): 0 
Gene Names: CCNKCPR4
UniProt & NIH Common Fund Data Resources
Find proteins for O75909 (Homo sapiens)
Explore O75909 
Go to UniProtKB:  O75909
PHAROS:  O75909
GTEx:  ENSG00000090061 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75909
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
B, E, H
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free:  0.250 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 249.521α = 90
b = 249.521β = 90
c = 218.535γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata 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 RMFClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyEXC2151-390873048

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release