6VDB: SETD2

Name: PDB 6VDB: SETD2 in complex with a H3-variant super-substrate peptide
Published: 2020-01-29
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

SETD2 in complex with a H3-variant super-substrate peptide. Determined by X-ray diffraction at 2.3 Å resolution. Released 29 Jan 2020.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 2,015
Mol. weight: 37.73 kDa
Ligands: SCN, ZN, SAH
Released: 29 Jan 2020

Explore 6VDB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VDB contains 16 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: 16 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	1451-1455	5
α-helix	1457-1465	9
α-helix	1470-1472	3
β-strand	1474-1475	2	1
β-strand	1480-1481	2	2
α-helix	1501-1505	5
α-helix	1506-1510	5
α-helix	1513-1514	2
β-strand	1515	1	3
α-helix	1521-1524	4
β-strand	1527	1	4
α-helix	1536-1538	3
β-strand	1539	1	3
β-strand	1552-1556	5	5
β-strand	1562-1566	5	5
β-strand	1570	1	6
β-strand	1575-1578	4	4
β-strand	1582-1584	3	2
α-helix	1586-1599	14
β-strand	1606-1610	5	2
β-strand	1613-1616	4	2
β-strand	1620-1621	2	1
α-helix	1623-1626	4
α-helix	1627	1
β-strand	1628-1629	2	7
β-strand	1635-1642	8	4
β-strand	1645-1652	8	4
β-strand	1656	1	6
α-helix	1660	1
β-strand	1661	1	5
α-helix	1662	1
β-strand	1663-1664	2	7
β-strand	1669-1670	2	8
α-helix	1675	1
β-strand	1676-1677	2	9
α-helix	1678	1
β-strand	1688-1689	2	9
α-helix	1697-1700	4

Chain H: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	34-35	2	8
β-strand	36	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase SETD2	A	protein	295	Homo sapiens	Q9BYW2 (AlphaFold model)
Ala-pro-arg-phe-gly-gly-val-met-arg-pro-asn-arg	H	protein	14	synthetic construct

Sequence of entity 1 (A), FASTA

>6VDB_1 Histone-lysine N-methyltransferase SETD2 (chains A)
MHHHHHHSSGRENLYFQGETSVPPGSALVGPSCVMDDFRDPQRWKECAKQGKMPCYFDLI
EENVYLTERKKNKSHRDIKRMQCECTPLSKDERAQGEIACGEDCLNRLLMIECSSRCPNG
DYCSNRRFQRKQHADVEVILTEKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEY
ARNKNIHYYFMALKNDEIIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLV
PSGSELTFDYQFQRYGKEAQKCFCGSANCRGYLGGENRVSIRAAGGKMKKERSRK

Sequence of entity 2 (H), FASTA

>6VDB_2 ALA-PRO-ARG-PHE-GLY-GLY-VAL-MET-ARG-PRO-ASN-ARG (chains H)
APRFGGVMRPNRYR

Ligands and cofactors

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

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

Primary citation

Sequence specificity analysis of the SETD2 protein lysine methyltransferase and discovery of a SETD2 super-substrate. Schuhmacher, M.K., Beldar, S., Khella, M.S. et al. Commun Biol (2020) 3:511-511. DOI 10.1038/s42003-020-01223-6 · 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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