6Y0A | pdb_00006y0a

CRYSTAL STRUCTURE OF CDK8-CycC IN COMPLEX WITH BI00690300

• PDB DOI: https://doi.org/10.2210/pdb6Y0A/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2020-02-07 Released: 2021-02-17 
• Deposition Author(s): Bader, G., Boettcher, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Human Cyclin-Dependent Kinase8/Cyclinc In Complex With Ligand 30180596

Boettcher, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 80.93 kDa 
• Atom Count: 5,358 
• Modeled Residue Count: 613 
• Deposited Residue Count: 689 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 8	A	406	Homo sapiens	Mutation(s): 0  Gene Names: CDK8 EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P49336 (Homo sapiens) Explore P49336  Go to UniProtKB:  P49336
PHAROS:  P49336 GTEx:  ENSG00000132964

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-C	B	283	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P24863 (Homo sapiens) Explore P24863  Go to UniProtKB:  P24863
PHAROS:  P24863 GTEx:  ENSG00000112237

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JRE (Subject of Investigation/LOI)	C [auth A]	6-[5-chloranyl-4-[(1~{S})-1-oxidanylethyl]pyridin-3-yl]-3,4-dihydro-2~{H}-1,8-naphthyridine-1-carboxamide C16 H17 Cl N4 O2 QDAISIXQQMBVSS-VIFPVBQESA-N
EDO	D [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	E [auth B], F [auth B], G [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.598	α = 90
b = 71.12	β = 90
c = 169.785	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Bader, G., Boettcher, J.

Revision History  

• Version 1.0: 2021-02-17
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.2: 2025-09-17
  Changes: Structure summary