3SVM: Human MPP8 - human DNMT3AK47me2 peptide

Name: PDB 3SVM: Human MPP8 - human DNMT3AK47me2 peptide
Published: 2011-11-30
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Human MPP8 - human DNMT3AK47me2 peptide. Determined by X-ray diffraction at 2.31 Å resolution. Released 30 Nov 2011.

Method: X-ray diffraction
Resolution: 2.31 Å
Organism: Homo sapiens
Chains: 2
Atoms: 604
Mol. weight: 9.05 kDa
Released: 30 Nov 2011

Explore 3SVM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3SVM contains 3 α-helices and 5 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: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	59-60	2	1
β-strand	61-70	10	2
β-strand	73-80	8	2
α-helix	85-87	3
β-strand	89-92	4	2
α-helix	93-95	3
α-helix	100-111	12

Chain P: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	44-45	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
M-phase phosphoprotein 8	A	protein	62	Homo sapiens	Q99549 (AlphaFold model)
DNA (cytosine-5)-methyltransferase 3A	P	protein	15	Homo sapiens	Q9Y6K1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3SVM_1 M-phase phosphoprotein 8 (chains A)
GEDVFEVEKILDMKTEGGKVLYKVRWKGYTSDDDTWEPEIHLEDCKEVLLEFRKKIAENK
AK

Sequence of entity 2 (P), FASTA

>3SVM_2 DNA (cytosine-5)-methyltransferase 3A (chains P)
YEPSTTARKVGRPGR

Primary citation

MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a. Chang, Y., Sun, L., Kokura, K. et al. Nat Commun (2011) 2:533-533. DOI 10.1038/ncomms1549 · PubMed

Other PDB entries of the same protein (UniProt Q99549 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6V2S 1.6 Å, Crystal Structure of chromodomain of MPP8 in complex with inhibitor UNC3866
9H77 2.01 Å, MPP8 chromodomain in complex with nanobody 3A02
7M5U 2.02 Å, Crystal structure of human MPP8 chromodomain in complex with peptidomimetic ligand UNC5246
3LWE 2.05 Å, The crystal structure of MPP8
3R93 2.06 Å, Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3…
3QO2 2.49 Å, Structural insights for MPP8 chromodomain interaction with histone H3 lysine 9
8QFB 3.04 Å, Crystal structure of human MPP8 C-terminal region (residues 565-860)

Browse structure collections

About this viewer

MolViewer shows 3SVM directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.