5W1Y: SETD8

SETD8 in complex with a covalent inhibitor. Determined by X-ray diffraction at 1.7 Å resolution. Released 21 Jun 2017.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,835
Mol. weight: 38.28 kDa
Ligands: 9SV
Released: 21 Jun 2017

Explore 5W1Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W1Y contains 15 α-helices and 26 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: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	236-253	18
β-strand	259-264	6	1
β-strand	268-273	6	1
β-strand	277	1	2
β-strand	282-286	5	3
β-strand	289-292	4	4
α-helix	293-303	11
β-strand	313-318	6	4
β-strand	321-326	6	4
α-helix	334-337	4
α-helix	338	1
β-strand	339-340	2	3
β-strand	346-353	8	3
β-strand	356-363	8	3
β-strand	367	1	2
α-helix	371	1
β-strand	372	1	1
α-helix	373	1
β-strand	374-375	2	3
α-helix	378-387	10
α-helix	389-392	4

Chain B: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	244-253	10
β-strand	259-264	6	5
β-strand	268-273	6	5
β-strand	277	1	6
β-strand	282-285	4	7
β-strand	289-292	4	8
α-helix	293-304	12
β-strand	313-318	6	8
β-strand	321-326	6	8
α-helix	335-337	3
α-helix	338	1
β-strand	339-340	2	7
β-strand	346-353	8	7
β-strand	356-363	8	7
β-strand	367	1	6
α-helix	371	1
β-strand	372	1	5
α-helix	373	1
β-strand	374-375	2	7
α-helix	378-387	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N-lysine methyltransferase KMT5A	A, B	protein	166	Homo sapiens	Q9NQR1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5W1Y_1 N-lysine methyltransferase KMT5A (chains A, B)
GAMGSRKSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYH
GDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKSGNCQ
TKLHDIDGVPHLILIASRDIAAGEELLYDYGDRSKASIEAHPWLKH

Ligands and cofactors

ID	Name	Formula	Copies
9SV	2-(4-methylpiperazin-1-yl)-3-(phenylsulfanyl)naphthalene-1,4-dione	C21 H20 N2 O2 S	2

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

Primary citation

SETD8 in complex with a covalent inhibitor. Tempel, W., Yu, W., Li, Y. et al. To be published.

Other PDB entries of the same protein (UniProt Q9NQR1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3F9X 1.25 Å, Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases,…
5TEG 1.3 Å, Crystal structure of hSETD8 in complex with histone H4K20 norleucine mutant peptide and…
1ZKK 1.45 Å, Crystal structure of hSET8 in ternary complex with H4 peptide (16-24) and AdoHcy
2BQZ 1.5 Å, Crystal structure of a ternary complex of the human histone methyltransferase Pr-SET7…
3F9Y 1.5 Å, Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases,…
3F9W 1.6 Å, Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases,…
3F9Z 1.6 Å, Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases,…
5TH7 1.95 Å, Complex of SETD8 with MS453
4IJ8 2.0 Å, Crystal structure of the complex of SETD8 with SAM
5V2N 2.0 Å, Crystal Structure of APO Human SETD8
9CR7 2.05 Å, Structure of human SETD8 in complex with covalent inhibitor AM2928
5T5G 2.1 Å, human SETD8 in complex with MS2177

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