5KCH

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

• PDB DOI: https://doi.org/10.2210/pdb5KCH/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-06-06 Released: 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.258 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 

Starting Model: experimental

Literature

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

Tempel, W., Harding, R.J., Mader, P., Dobrovetsky, E., Walker, J.R., Brown, P.J., Schapira, M., Arrowsmith, C.H., Edwards, A.M., Santhakumar, S., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42.94 kDa 
• Atom Count: 1,910 
• Modelled Residue Count: 212 
• Deposited Residue Count: 225 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SETDB1	A	225	Homo sapiens	Mutation(s): 0  Gene Names: SETDB1, KIAA0067, KMT1E EC: 2.1.1.43 (PDB Primary Data), 2.1.1.366 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q15047 (Homo sapiens) Explore Q15047  Go to UniProtKB:  Q15047
PHAROS:  Q15047 GTEx:  ENSG00000143379

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6RN	CB [auth A]	4-methoxy-N-[(pyridin-2-yl)methyl]aniline C13 H14 N2 O VZYUNDIQWDHYLW-UHFFFAOYSA-N
SO4	AB [auth A], BB [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	ZA [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
UNX	AA [auth A], B [auth A], BA [auth A], C [auth A], CA [auth A], D [auth A], DA [auth A], E [auth A], EA [auth A], F [auth A], FA [auth A], G [auth A], GA [auth A], H [auth A], HA [auth A], I [auth A], IA [auth A], J [auth A], JA [auth A], K [auth A], KA [auth A], L [auth A], LA [auth A], M [auth A], MA [auth A], N [auth A], NA [auth A], O [auth A], OA [auth A], P [auth A], PA [auth A], Q [auth A], QA [auth A], R [auth A], RA [auth A], S [auth A], SA [auth A], T [auth A], TA [auth A], U [auth A], UA [auth A], V [auth A], VA [auth A], W [auth A], WA [auth A], X [auth A], XA [auth A], Y [auth A], YA [auth A], Z [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.258 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M35KCH

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.967	α = 90
b = 63.607	β = 90
c = 70.457	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Structure summary
• Version 2.0: 2019-02-20
  Changes: Advisory, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description