5WBV: SET Domain of Human SUV420H1

Crystal Structure of the SET Domain of Human SUV420H1 In Complex With Inhibitor. Determined by X-ray diffraction at 2.3 Å resolution. Released 19 Jul 2017.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,586
Mol. weight: 64.89 kDa
Ligands: 9ZY, SAM, ZN
Released: 19 Jul 2017

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

Secondary structure: helices and β-sheets

5WBV contains 27 α-helices and 24 β-strands across 2 chains. 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	74-88	15
α-helix	90-93	4
α-helix	96-98	3
α-helix	132-147	16
α-helix	150-157	8
α-helix	161-166	6
α-helix	172-187	16
β-strand	195-200	6	1
β-strand	209-214	6	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	322-326	5

Chain B: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	74-88	15
α-helix	90-93	4
α-helix	133-147	15
α-helix	150-157	8
α-helix	172-187	16
β-strand	195-200	6	5
β-strand	209-214	6	5
β-strand	218	1	6
β-strand	223-234	12	7
α-helix	236-242	7
β-strand	252-255	4	7
β-strand	260-265	6	7
α-helix	267-270	4
α-helix	271	1
β-strand	272-273	2	8
β-strand	279-283	5	7
β-strand	288-293	6	7
β-strand	297	1	6
α-helix	301	1
β-strand	302	1	5
α-helix	303	1
β-strand	304-305	2	8
α-helix	314-316	3
α-helix	322-326	5
α-helix	330-332	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase KMT5B	A, B	protein	273	Homo sapiens	Q4FZB7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5WBV_1 Histone-lysine N-methyltransferase KMT5B (chains A, B)
QSRYVPSSGMSAKELCENDDLATSLVLDPYLGFQTHKMNTSAFPSRSSRHFSKSDSFSHN
NPVRFRPIKGRQEELKEVIERFKKDEHLEKAFKCLTSGEWARHYFLNKNKMQEKLFKEHV
FIYLRMFATDSGFEILPCNRYSSEQNGAKIVATKEWKRNDKIELLVGCIAELSEIEENML
LRHGENDFSVMYSTRKNCAQLWLGPAAFINHDCRPNCKFVSTGRDTACVKALRDIEPGEE
ISCYYGDGFFGENNEFCECYTCERRGTGAFKSR

Ligands and cofactors

ID	Name	Formula	Copies
9ZY	2-chloro-5-(4-methyl-6-oxo-3-phenylpyrano[2,3-c]pyrazol-1(6H)-yl)benzoic acid	C20 H13 Cl N2 O4	2
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	2
ZN	Zinc ion	Zn	2

Water and common crystallization additives (UNX) are not listed.

Primary citation

Crystal Structure of the SET Domain of Human SUV420H1 In Complex With Inhibitor. Halabelian, L., Tempel, W., 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…
8T68 1.9 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
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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