6CBX | pdb_00006cbx

Crystal structure of human SET and MYND Domain Containing protein 2 with MTF1497

• PDB DOI: https://doi.org/10.2210/pdb6CBX/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2018-02-05 Released: 2018-03-14 
• Deposition Author(s): ZENG, H., DONG, A., Hutchinson, A., Seitova, A., TATLOCK, J., KUMPF, R., OWEN, A., TAYLOR, A., Casimiro-Garcia, A., Bountra, C., Arrowsmith, C.H., Edwards, A.M., BROWN, P.J., WU, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.223 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.180 (Depositor) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Crystal structure of human SET and MYND Domain Containing protein 2 with MTF1497

ZENG, H., DONG, A., Hutchinson, A., Seitova, A., TATLOCK, J., KUMPF, R., OWEN, A., TAYLOR, A., Casimiro-Garcia, A., Bountra, C., Arrowsmith, C.H., Edwards, A.M., BROWN, P.J., WU, H., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 101.47 kDa 
• Atom Count: 7,344 
• Modeled Residue Count: 861 
• Deposited Residue Count: 868 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-lysine methyltransferase SMYD2	A, B	434	Homo sapiens	Mutation(s): 0  Gene Names: SMYD2, KMT3C EC: 2.1.1 (PDB Primary Data), 2.1.1.43 (PDB Primary Data), 2.1.1.354 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRG4 (Homo sapiens) Explore Q9NRG4  Go to UniProtKB:  Q9NRG4
PHAROS:  Q9NRG4 GTEx:  ENSG00000143499

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EW1	F [auth A], R [auth B]	[3-(4-amino-6-methyl-1H-imidazo[4,5-c]pyridin-1-yl)azetidin-1-yl][1-({1-[(1R)-cyclohept-2-en-1-yl]piperidin-4-yl}methyl )-1H-pyrrol-3-yl]methanone C28 H37 N7 O HQHAEFHJXLPTMM-QHCPKHFHSA-N
ZN	C [auth A], D [auth A], E [auth A], O [auth B], P [auth B], Q [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	H [auth A], I [auth A], T [auth B], U [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	G [auth A], S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNX	J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.223 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.180 (Depositor) 
• R-Value Observed: 0.181 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36cbx

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.02	α = 90
b = 117.031	β = 92.54
c = 64.444	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-14 
Deposition Author(s): ZENG, H., DONG, A., Hutchinson, A., Seitova, A., TATLOCK, J., KUMPF, R., OWEN, A., TAYLOR, A., Casimiro-Garcia, A., Bountra, C., Arrowsmith, C.H., Edwards, A.M., BROWN, P.J., WU, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2018-03-14
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references, Derived calculations, Structure summary