5KH6 | pdb_00005kh6

SETDB1 in complex with a fragment candidate

• PDB DOI: https://doi.org/10.2210/pdb5KH6/pdb

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


• Deposited: 2016-06-14 Released: 2016-09-21 
• Deposition Author(s): Walker, J.R., Harding, R.J., Mader, P., Dobrovetsky, E., Dong, A., Collins, P., Pearce, N., Brandao-Neto, J., Douangamath, A., von Delft, F., Brown, P.J., Schapira, M., Arrowsmith, C.H., Edwards, A.M., Santhakumar, V., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

SETDB1 in complex with a fragment candidate

Walker, J.R., Harding, R.J., Mader, P., Dobrovetsky, E., Dong, A., Collins, P., Pearce, N., Brandao-Neto, J., Douangamath, A., von Delft, F., Brown, P.J., Schapira, M., Arrowsmith, C.H., Edwards, A.M., Santhakumar, V., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 26.27 kDa 
• Atom Count: 2,017 
• Modeled Residue Count: 211 
• Deposited Residue Count: 211 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SETDB1	A	211	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 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6SU	N [auth A]	methyl 3-(methylsulfonylamino)benzoate C9 H11 N O4 S UQIOKJVVJMHUTP-UHFFFAOYSA-N
PEG	P [auth A], Q [auth A], R [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	U [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	B [auth A], D [auth A], O [auth A], T [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	S [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	J [auth A], K [auth A], L [auth A], M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.76	α = 90
b = 63.81	β = 90
c = 70.31	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
autoXDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-21 
Deposition Author(s): Walker, J.R., Harding, R.J., Mader, P., Dobrovetsky, E., Dong, A., Collins, P., Pearce, N., Brandao-Neto, J., Douangamath, A., von Delft, F., Brown, P.J., Schapira, M., Arrowsmith, C.H., Edwards, A.M., Santhakumar, V., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2016-09-21
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-04-03
  Changes: Refinement description