3RGF

Crystal Structure of human CDK8/CycC

Structural Biology Knowledgebase: 3RGF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.181

Literature

Macromolecules
Sequence Display for 3RGF

Classification: TRANSFERASE TRANSCRIPTION

Total Structure Weight: 81711.12

Macromolecule Entities
Molecule Chains Length Organism Details
Cyclin-dependent kinase 8 A 405 Homo sapiens EC#: 2.7.11.22 IUBMB 2.7.11.23 IUBMB
Fragment: UNP residues 1-403
Gene Name(s): CDK8 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cyclin-C B 285 Homo sapiens Gene Name(s): CCNC Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BAX
Query on BAX

A 4-{4-[({[4-CHLORO-3-(TRIFLUOROMETHYL)PHENYL]AMINO}CARBONYL)AMINO]PHENOXY}- N-METHYLPYRIDINE-2-CARBOXAMIDE
Sorafenib (Synonym)
C21 H16 Cl F3 N4 O3
MLDQJTXFUGDVEO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BAX Kd: 250 - 310000 nM (91 - 100) BindingDB

IC50: 130 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.181
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.69 α = 90.00
b = 70.61 β = 108.31
c = 79.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-04-08
  • Released Date: 2011-08-10
  • Deposition author(s): Schneider, E.V., Boettcher, J., Blaesse, M., Huber, R., Maskos, K.

Revision History

  • 2012-10-03
    Type: Non-polymer description | Details: Ligand synonym added
  • 2011-09-07
    Type: Citation | Details: Citation update