8BU5

Structure of DDB1 bound to SR-4835-engaged CDK12-cyclin K

  • Classification: LIGASE
  • Organism(s): Homo sapiens
  • Expression System: Trichoplusia ni
  • Mutation(s): Yes 

  • Deposited: 2022-11-30 Released: 2023-09-13 
  • Deposition Author(s): Kozicka, Z., Kempf, G., Petzold, G., Thoma, N.H.
  • Funding Organization(s): European Research Council (ERC), Swiss National Science Foundation, Swiss Cancer League, Marie Sklodowska-Curie Actions, FragNET ITN, Other private

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

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Literature

Structure of DDB1 bound to DS17-engaged CDK12-cyclin K

Kozicka, Z., Kempf, G., Petzold, G., Thoma, N.H.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA damage-binding protein 1
A, D, G
840Homo sapiensMutation(s): 0 
Gene Names: DDB1, XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens)
Explore Q16531 
Go to UniProtKB:  Q16531
PHAROS:  Q16531
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16531
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase 12
B, E, H
344Homo sapiensMutation(s): 1 
Gene Names: CDK12, CRK7, CRKRS, KIAA0904
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
Entity Groups  
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UniProt GroupQ9NYV4
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-K
C, F, I
271Homo sapiensMutation(s): 0 
Gene Names: CCNK, CPR4
UniProt & NIH Common Fund Data Resources
Find proteins for O75909 (Homo sapiens)
Explore O75909 
Go to UniProtKB:  O75909
PHAROS:  O75909
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75909
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RMF (Subject of Investigation/LOI)
Query on RMF
Download Ideal Coordinates CCD File 
K [auth B],
M [auth E],
P [auth H]		~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine
C21 H20 Cl2 N10 O
FSELUFUYNUNZKD-UHFFFAOYSA-N		 Ligand Interaction
CIT
Query on CIT
Download Ideal Coordinates CCD File 
L [auth C],
N [auth F],
R [auth I]		CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
J [auth A],
O [auth G],
Q [auth H]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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: 3.13 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 249.938α = 90
b = 249.938β = 90
c = 219.302γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Cootmodel building
STARANISOdata scaling
autoPROCdata processing
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union666068
Swiss National Science FoundationSwitzerland31003A_179541
Swiss National Science FoundationSwitzerland310030_301206
Swiss Cancer LeagueSwitzerland4980-02-2020
Swiss National Science FoundationSwitzerlandCRSII5_186230
Marie Sklodowska-Curie Actions, FragNET ITNEuropean Union765445
Other privateSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-13
    Type: Initial release