5TH7: Complex of SETD8 with MS453

Name: PDB 5TH7: Complex of SETD8 with MS453
Published: 2016-11-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Complex of SETD8 with MS453. Determined by X-ray diffraction at 1.95 Å resolution. Released 9 Nov 2016.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,366
Mol. weight: 34.4 kDa
Ligands: 7BY
Released: 9 Nov 2016

Explore 5TH7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5TH7 contains 12 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: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	238-253	16
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	289-292	4	4
α-helix	293-302	10
α-helix	307-309	3
β-strand	313-318	6	4
β-strand	321-326	6	4
α-helix	335-337	3
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	372-373	2	1
β-strand	374-375	2	3

Chain B: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	237-251	15
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	289-291	3	8
α-helix	293-303	11
α-helix	307-309	3
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	374-376	3	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N-lysine methyltransferase KMT5A	A, B	protein	148	Homo sapiens	Q9NQR1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5TH7_1 N-lysine methyltransferase KMT5A (chains A, B)
GKSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHGDLIE
ITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKSGNCQTKLHD
IDGVPHLILIASRDIAAGEELLYDYGDR

Ligands and cofactors

ID	Name	Formula	Copies
7BY	N-(3-{[6,7-dimethoxy-2-(pyrrolidin-1-yl)quinazolin-4-yl]amino}propyl)propanamide	C20 H29 N5 O3	2

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

Primary citation

Structure-Based Design of a Covalent Inhibitor of the SET Domain-Containing Protein 8 (SETD8) Lysine Methyltransferase. Butler, K.V., Ma, A., Yu, W. et al. J Med Chem (2016) 59:9881-9889. DOI 10.1021/acs.jmedchem.6b01244 · 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,…
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
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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