5V2N: APO Human SETD8

Name: PDB 5V2N: Crystal Structure of APO Human SETD8
Published: 2018-03-07
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal Structure of APO Human SETD8. Determined by X-ray diffraction at 2.0 Å resolution. Released 7 Mar 2018.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,404
Mol. weight: 18.69 kDa
Released: 7 Mar 2018

Explore 5V2N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V2N contains 8 α-helices and 13 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: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	192-194	3
α-helix	195-212	18
β-strand	218-223	6	1
β-strand	227-232	6	1
β-strand	236	1	2
β-strand	241-244	4	3
β-strand	248-252	5	4
α-helix	255-262	8
β-strand	273-277	5	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	340-345	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N-lysine methyltransferase KMT5A	A	protein	165	Homo sapiens	Q9NQR1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5V2N_1 N-lysine methyltransferase KMT5A (chains A)
GGSSRKSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHG
DLIEITDAAARAALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKCGNCQT
KLHDIDGVPHLILIASRDIAAGEELLYDYGDRSKASIEAHPWLKH

Primary citation

The dynamic conformational landscape of the protein methyltransferase SETD8. Chen, S., Wiewiora, R.P., Meng, F. et al. Elife (2019) 8. DOI 10.7554/eLife.45403 · 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
5TH7 1.95 Å, Complex of SETD8 with MS453
4IJ8 2.0 Å, Crystal structure of the complex of SETD8 with SAM
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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