8T68: Histone-lysine N-methyltransferase KMT5B

Crystal Structure of the SET Domain of Human Histone-Lysine N-Methyltransferase SUV420H1 in complex with RQ3-111. Determined by X-ray diffraction at 1.9 Å resolution. Released 27 Nov 2024.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,968
Mol. weight: 32.48 kDa
Ligands: ZKI, SAM, ZN
Released: 27 Nov 2024

Explore 8T68 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T68 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 A: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	74-93	20
α-helix	132-147	16
α-helix	150-157	8
α-helix	161-167	7
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	252-253	2	3
β-strand	261-265	5	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 KMT5B	A	protein	274	Homo sapiens	Q4FZB7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8T68_1 Histone-lysine N-methyltransferase KMT5B (chains A)
GQSRYVPSSGMSAKELCENDDLATSLVLDPYLGFQTHKMNTSAFPSRSSRHFSKSDSFSH
NNPVRFRPIKGRQEELKEVIERFKKDEHLEKAFKCLTSGEWARHYFLNKNKMQEKLFKEH
VFIYLRMFATDSGFEILPCNRYSSEQNGAKIVATKEWKRNDKIELLVGCIAELSEIEENM
LLRHGENDFSVMYSTRKNCAQLWLGPAAFINHDCRPNCKFVSTGRDTACVKALRDIEPGE
EISCYYGDGFFGENNEFCECYTCERRGTGAFKSR

Ligands and cofactors

ID	Name	Formula	Copies
ZKI	6,7-dichloro-N-[(3R)-oxolan-3-yl]-4-(pyridin-4-yl)phthalazin-1-amine	C17 H14 Cl2 N4 O	1
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	1
ZN	Zinc ion	Zn	1

Primary citation

Crystal Structure of the SET Domain of Human Histone-Lysine N-Methyltransferase SUV420H1 in complex with RQ3-111. Zeng, H., Dong, A., Brown, P.J. et al. To be published.

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…
5CPR 2.22 Å, The novel SUV4-20 inhibitor A-196 verifies a role for epigenetics in genomic integrity
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

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