4H12: Histone-lysine N-methyltransferase SETD2

Name: PDB 4H12: The crystal structure of methyltransferase domain of human SET domain-containing protein 2 in complex with S-adenosyl-L-homocysteine
Published: 2012-10-03
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

The crystal structure of methyltransferase domain of human SET domain-containing protein 2 in complex with S-adenosyl-L-homocysteine. Determined by X-ray diffraction at 2.06 Å resolution. Released 3 Oct 2012.

Method: X-ray diffraction
Resolution: 2.06 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,940
Mol. weight: 32.57 kDa
Ligands: ZN, SAH
Released: 3 Oct 2012

Explore 4H12 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4H12 contains 12 α-helices and 21 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: 12 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	1448-1450	3	1
α-helix	1451-1455	5
α-helix	1457-1465	9
α-helix	1470-1472	3
β-strand	1474-1475	2	2
β-strand	1480-1481	2	3
α-helix	1501-1505	5
α-helix	1506-1511	6
α-helix	1513-1514	2
α-helix	1523-1525	3
β-strand	1527	1	4
α-helix	1536-1538	3
β-strand	1552-1556	5	1
β-strand	1562-1566	5	1
β-strand	1570	1	5
β-strand	1575-1578	4	4
β-strand	1582-1584	3	3
α-helix	1586-1598	13
β-strand	1606-1610	5	3
β-strand	1613-1616	4	3
β-strand	1620-1621	2	2
α-helix	1623-1626	4
α-helix	1627	1
β-strand	1628-1629	2	6
β-strand	1635-1642	8	4
β-strand	1645-1652	8	4
β-strand	1656	1	5
α-helix	1660	1
β-strand	1661-1662	2	1
β-strand	1663-1664	2	6
β-strand	1670-1671	2	3
β-strand	1676-1677	2	7
β-strand	1688-1689	2	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase SETD2	A	protein	278	Homo sapiens	Q9BYW2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4H12_1 Histone-lysine N-methyltransferase SETD2 (chains A)
GETSVPPGSALVGPSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLTERKKNKSHRD
IKRMQCECTPLSKDERAQGEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVE
VILTEKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMALKNDE
IIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLVPSGSELTFDYQFQRYGK
EAQKCFCGSANCRGYLGGENRVSIRAAGGKMKKERSRK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	1

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

Primary citation

Sinefungin Derivatives as Inhibitors and Structure Probes of Protein Lysine Methyltransferase SETD2. Zheng, W., Ibanez, G., Wu, H. et al. J Am Chem Soc (2012) 134:18004-18014. DOI 10.1021/ja307060p · PubMed

Other PDB entries of the same protein (UniProt Q9BYW2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5JLB 1.5 Å, Crystal structure of SETD2 bound to histone H3.3 K36I peptide
5LT7 1.51 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
5LT8 1.57 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
7EVS 1.6 Å, Crystal structure of hnRNP LL RRM2 in complex with SETD2
5LSY 1.62 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
5LSZ 1.62 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
9G4A 1.65 Å, Structure of human SETD2 T1663M mutant in complex with SAM and H3K36M peptide
6J9J 1.78 Å, crystal structure of SESTD2 in complex with H3.3S31phK36M peptide
5LSS 1.79 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
7EVR 1.8 Å, Crystal structure of hnRNP L RRM2 in complex with SETD2
7LZD 1.8 Å, Crystal Structure of SETD2 bound to Compound 35
8Q5P 1.81 Å, Structure of the lysine methyltransferase SETD2 in complex with a peptide derived from…

Browse structure collections

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