5KCH

SETDB1 in complex with an early stage, low affinity fragment candidate modelled at reduced occupancy into weak electron density


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.215

Literature

Macromolecules
Sequence Display for 5KCH

Classification: TRANSFERASE

Total Structure Weight: 42925.74

Macromolecule Entities
Molecule Chains Length Organism Details
Histone-lysine N-methyltransferase SETDB1 A 225 Homo sapiens EC#: 2.1.1.43 IUBMB
Fragment: UNP residues 196-403
Gene Name(s): SETDB1 Gene View KIAA0067 KMT1E
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
6RN
Query on 6RN

A 4-(pyridin-2-ylmethylamino)phenol
C12 H12 N2 O
MWVZFGXUCTUKOC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

A DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UNX
Query on UNX

A UNKNOWN ATOM OR ION
X
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 55.97 α = 90.00
b = 63.61 β = 90.00
c = 70.46 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-06-06
  • Released Date: 2016-07-27
  • Deposition author(s): Tempel, W., Harding, R.J., Mader, P., Dobrovetsky, E., Walker, J.R., Brown, P.J., Schapira, M., Collins, P., Pearce, N., Brandao-Neto, J., Douangamath, A., von Delft, F., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Santhakumar, V., Structural Genomics Consortium (SGC)

Revision History

  • Version 1_0: 2016-07-27

    Type: Initial release

  • Version 1_1: 2017-01-25

    Type: Structure summary