5TEG: HSETD8

Name: PDB 5TEG: Crystal structure of hSETD8 in complex with histone H4K20 norleucine mutant peptide and S-Adenosylmethionine
Published: 2016-12-07
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of hSETD8 in complex with histone H4K20 norleucine mutant peptide and S-Adenosylmethionine. Determined by X-ray diffraction at 1.3 Å resolution. Released 7 Dec 2016.

Method: X-ray diffraction
Resolution: 1.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,066
Mol. weight: 39.39 kDa
Ligands: SAM
Released: 7 Dec 2016

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

Secondary structure: helices and β-sheets

5TEG contains 16 α-helices and 28 β-strands across 4 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	195-212	18
β-strand	218-223	6	1
β-strand	227-232	6	1
β-strand	236	1	2
β-strand	241-245	5	3
β-strand	248-251	4	4
α-helix	252-262	11
β-strand	272-277	6	4
β-strand	280-285	6	4
α-helix	294-296	3
α-helix	297	1
β-strand	298-299	2	5
β-strand	305-312	8	3
β-strand	315-322	8	3
β-strand	326	1	2
α-helix	330	1
β-strand	331	1	1
α-helix	332	1
β-strand	333-334	2	5
α-helix	341-346	6
α-helix	348-351	4

Chain B: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	196-212	17
β-strand	218-223	6	6
β-strand	227-232	6	6
β-strand	236	1	7
β-strand	241-245	5	8
β-strand	248-251	4	9
α-helix	252-263	12
β-strand	272-277	6	9
β-strand	280-285	6	9
α-helix	294-296	3
α-helix	297	1
β-strand	298-299	2	10
β-strand	305-312	8	8
β-strand	315-322	8	8
β-strand	326	1	7
α-helix	330	1
β-strand	331	1	6
α-helix	332	1
β-strand	333-334	2	10
α-helix	341-346	6
α-helix	348-351	4

Chains D and E: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	20-21	2	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N-lysine methyltransferase KMT5A	A, B	protein	160	Homo sapiens	Q9NQR1 (AlphaFold model)
Histone H4 mutant peptide with H4K20norleucine	D, E	protein	8	Homo sapiens	P62805 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5TEG_1 N-lysine methyltransferase KMT5A (chains A, B)
KSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHGDLIEI
TDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKSGNCQTKLHDI
DGVPHLILIASRDIAAGEELLYDYGDRSKASIEAHPWLKH

Sequence of entity 2 (D, E), FASTA

>5TEG_2 Histone H4 mutant peptide with H4K20norleucine (chains D, E)
KRHRLVLR

Ligands and cofactors

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

Primary citation

Turning a Substrate Peptide into a Potent Inhibitor for the Histone Methyltransferase SETD8. Judge, R.A., Zhu, H., Upadhyay, A.K. et al. ACS Med Chem Lett (2016) 7:1102-1106. DOI 10.1021/acsmedchemlett.6b00303 · PubMed

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,…
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
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

Browse structure collections

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