5CPR: Histone-lysine N-methyltransferase SUV420H1

Name: PDB 5CPR: The novel SUV4-20 inhibitor A-196 verifies a role for epigenetics in genomic integrity
Published: 2017-01-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

The novel SUV4-20 inhibitor A-196 verifies a role for epigenetics in genomic integrity. Determined by X-ray diffraction at 2.22 Å resolution. Released 25 Jan 2017.

Method: X-ray diffraction
Resolution: 2.22 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,014
Mol. weight: 31.75 kDa
Ligands: ZN, SAM, 539
Released: 25 Jan 2017

Explore 5CPR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5CPR contains 14 α-helices and 12 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain B: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	74-93	20
α-helix	134-147	14
α-helix	150-157	8
α-helix	164-167	4
α-helix	172-186	15
α-helix	187-189	3
β-strand	195-199	5	1
β-strand	210-214	5	1
β-strand	218	1	2
β-strand	223-234	12	3
α-helix	236-242	7
β-strand	252-255	4	3
β-strand	260-265	6	3
α-helix	267-270	4
α-helix	271	1
β-strand	272-273	2	4
β-strand	279-283	5	3
β-strand	288-293	6	3
β-strand	297	1	2
α-helix	301	1
β-strand	302	1	1
α-helix	303	1
β-strand	304-305	2	4
α-helix	314-316	3
α-helix	322-327	6
α-helix	330-332	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase SUV420H1	B	protein	268	Homo sapiens	Q4FZB7 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>5CPR_1 Histone-lysine N-methyltransferase SUV420H1 (chains B)
GSSGMSAKELCENDDLATSLVLDPYLGFQTHKMNTSAFPSRSSRHFSKSDSFSHNNPVRF
RPIKGRQEELKEVIERFKKDEHLEKAFKCLTSGEWARHYFLNKNKMQEKLFKEHVFIYLR
MFATDSGFEILPCNRYSSEQNGAKIVATKEWKRNDKIELLVGCIAELSEIEENMLLRHGE
NDFSVMYSTRKNCAQLWLGPAAFINHDCRPNCKFVSTGRDTACVKALRDIEPGEEISCYY
GDGFFGENNEFCECYTCERRGTGAFKSR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	1
539	6,7-dichloro-N-cyclopentyl-4-(pyridin-4-yl)phthalazin-1-amine	C18 H16 Cl2 N4	1

Primary citation

The SUV4-20 inhibitor A-196 verifies a role for epigenetics in genomic integrity. Bromberg, K.D., Mitchell, T.R., Upadhyay, A.K. et al. Nat Chem Biol (2017) 13:317-324. DOI 10.1038/nchembio.2282 · PubMed

Other PDB entries of the same protein (UniProt Q4FZB7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3S8P 1.85 Å, Crystal Structure of the SET Domain of Human Histone-Lysine N-Methyltransferase SUV420H1…
8T68 1.9 Å, Crystal Structure of the SET Domain of Human Histone-Lysine N-Methyltransferase SUV420H1…
5WBV 2.3 Å, Crystal Structure of the SET Domain of Human SUV420H1 In Complex With Inhibitor
8T9F 2.6 Å, Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1
7YRD 3.2 Å, histone methyltransferase
8T9H 3.37 Å, Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1
8JHG 3.58 Å, Native SUV420H1 bound to 167-bp nucleosome
8JHF 3.68 Å, Native SUV420H1 bound to 167-bp nucleosome
7YRG 4.2 Å, histone methyltransferase

Browse structure collections

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