5QT1 | pdb_00005qt1

PanDDA analysis group deposition -- Partial occupancy interpretation of PanDDA event map: SETDB1 in complex with FMOMB000017a

• PDB DOI: https://doi.org/10.2210/pdb5QT1/pdb
• Deposition Group: G_1002089 (changed state) | Explore  G_1002089  

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


• Deposited: 2019-06-25 Released: 2019-08-21 
• Deposition Author(s): Harding, R.J., Tempel, W., DOUANGAMATH, A., BRANDAO-NETO, J., Collins, P.M., Krojer, T., Mader, P., Schapira, M., von Delft, F., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Santhakumar, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.220 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

PanDDA analysis group deposition

Harding, R.J., Tempel, W., DOUANGAMATH, A., BRANDAO-NETO, J., Collins, P.M., Krojer, T., Mader, P., Schapira, M., von Delft, F., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Santhakumar, V.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.9 kDa 
• Atom Count: 1,980 
• Modeled Residue Count: 211 
• 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, ESET, 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DSJ (Subject of Investigation/LOI)	E [auth A]	1-(4-amino-2-hydroxyphenyl)ethan-1-one C8 H9 N O2 QQZFVONVJPXCSQ-UHFFFAOYSA-N
SO4	RA [auth A], SA [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	B [auth A], C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNX	AA [auth A], BA [auth A], CA [auth A], DA [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], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.220 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m3.irrmc.4136

Diffraction Data: https://doi.org/10.18430/m3.irrmc.4202

Diffraction Data: https://doi.org/10.18430/m3.irrmc.c.1

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.79	α = 90
b = 64.05	β = 90
c = 70.81	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-08-21 
Deposition Author(s): Harding, R.J., Tempel, W., DOUANGAMATH, A., BRANDAO-NETO, J., Collins, P.M., Krojer, T., Mader, P., Schapira, M., von Delft, F., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Santhakumar, V.

Revision History  

• Version 1.0: 2019-08-21
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references
• Version 1.2: 2026-02-18
  Changes: Derived calculations, Refinement description, Structure summary