6V2S: Chromodomain of MPP8

Crystal Structure of chromodomain of MPP8 in complex with inhibitor UNC3866. Determined by X-ray diffraction at 1.6 Å resolution. Released 25 Dec 2019.

Method: X-ray diffraction
Resolution: 1.6 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 1,235
Mol. weight: 18.77 kDa
Released: 25 Dec 2019

Explore 6V2S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6V2S contains 6 α-helices and 10 β-strands across 4 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	58-59	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	93-96	4
α-helix	100-113	14

Chain B: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	58-59	2	3
β-strand	61-70	10	4
β-strand	73-80	8	4
α-helix	85-87	3
β-strand	89-92	4	4
α-helix	93-99	7
α-helix	100-115	16

Chains C and D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-4	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
M-phase phosphoprotein 8	A, B	protein	62	Homo sapiens	Q99549 (AlphaFold model)
UNC3866	C, D	protein	6	synthetic construct

Sequence of entity 1 (A, B), FASTA

>6V2S_1 M-phase phosphoprotein 8 (chains A, B)
GEDVFEVEKILDMKTEGGKVLYKVRWKGYTSDDDTWEPEIHLEDCKEVLLEFRKKIAENK
AK

Sequence of entity 2 (C, D), FASTA

>6V2S_2 UNC3866 (chains C, D)
XFALXX

Primary citation

Structural Basis for the Binding Selectivity of Human CDY Chromodomains. Dong, C., Liu, Y., Lyu, T.J. et al. Cell Chem Biol (2020) 27:827-838.e7. DOI 10.1016/j.chembiol.2020.05.007 · PubMed

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

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…
3SVM 2.31 Å, Human MPP8 - human DNMT3AK47me2 peptide
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

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