4IJ8: Complex of SETD8 with SAM

Crystal structure of the complex of SETD8 with SAM. Determined by X-ray diffraction at 2.0 Å resolution. Released 16 Jan 2013.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, unidentified
Chains: 3
Atoms: 2,675
Mol. weight: 39.1 kDa
Ligands: SAM
Released: 16 Jan 2013

Explore 4IJ8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4IJ8 contains 20 α-helices and 26 β-strands across 3 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: 9 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	282-285	4	3
β-strand	289-293	5	4
α-helix	296-304	9
α-helix	306-309	4
α-helix	310-312	3
β-strand	313-318	6	4
β-strand	321-326	6	4
α-helix	335-337	3
β-strand	339-340	2	5
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	5
α-helix	382-387	6
α-helix	389-392	4

Chain B: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	245-253	9
β-strand	259-264	6	6
β-strand	268-273	6	6
β-strand	277	1	7
β-strand	282-285	4	8
β-strand	289-293	5	9
α-helix	296-304	9
α-helix	306-309	4
α-helix	310-312	3
β-strand	313-318	6	9
β-strand	321-326	6	9
α-helix	335-337	3
α-helix	338	1
β-strand	339-340	2	10
β-strand	346-353	8	8
β-strand	356-363	8	8
β-strand	367	1	7
α-helix	371	1
β-strand	372	1	6
α-helix	373	1
β-strand	374-375	2	10
α-helix	382-387	6
α-helix	389-392	4

Chain I: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-11	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N-lysine methyltransferase SETD8	A, B	protein	165	Homo sapiens	Q9NQR1 (AlphaFold model)
helical peptide	I	protein	10	unidentified

Sequence of entity 1 (A, B), FASTA

>4IJ8_1 N-lysine methyltransferase SETD8 (chains A, B)
AMGSRKSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHG
DLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKSGNCQT
KLHDIDGVPHLILIASRDIAAGEELLYDYGDRSKASIEAHPWLKH

Sequence of entity 2 (I), FASTA

>4IJ8_2 helical peptide (chains I)
XXXXXXXXXX

Ligands and cofactors

ID	Name	Formula	Copies
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	2

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

Primary citation

Crystal structure of the complex of SETD8 with SAM. Yu, W., Tempel, 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,…
5W1Y 1.7 Å, SETD8 in complex with a covalent inhibitor
5TH7 1.95 Å, Complex of SETD8 with MS453
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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