9H77: MPP8 chromodomain

MPP8 chromodomain in complex with nanobody 3A02. Determined by X-ray diffraction at 2.01 Å resolution. Released 5 Nov 2025.

Method: X-ray diffraction
Resolution: 2.01 Å
Organisms: Lama glama, Homo sapiens
Chains: 4
Atoms: 2,831
Mol. weight: 42.32 kDa
Released: 5 Nov 2025

Explore 9H77 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9H77 contains 12 α-helices and 28 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.

Chains A and B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	1
β-strand	14-16	3	2
β-strand	22-29	8	1
α-helix	33-35	3
β-strand	37-43	7	2
β-strand	50-55	6	2
β-strand	61-63	3	2
α-helix	65-67	3
β-strand	71-76	6	1
β-strand	81-86	6	1
α-helix	91-93	3
β-strand	95-102	8	2
β-strand	110-113	4	2
β-strand	117-121	5	2

Chain C: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	61-70	10	5
β-strand	73-80	8	5
α-helix	85-87	3
β-strand	89-92	4	5
α-helix	93-99	7
α-helix	100-114	15

Chain D: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	61-70	10	6
β-strand	73-80	8	6
α-helix	85-87	3
β-strand	89-92	4	6
α-helix	94-99	6
α-helix	100-114	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nb 3A02	A, B	protein	122	Lama glama
M-phase phosphoprotein 8	C, D	protein	68	Homo sapiens	Q99549 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9H77_1 Nb 3A02 (chains A, B)
GAMAQVQLQENGGGLVKPGGSLRLSCAASGFTLSDYVMTWVRQAPGKGPEWVSRISAGGS
TRYVDSVKGRFTISRDNAKNTMYLQMNSLKPEDTAVYYCARGSTLFSTNWDYRGQGTQVM
VS

Sequence of entity 2 (C, D), FASTA

>9H77_2 M-phase phosphoprotein 8 (chains C, D)
GAMEDGEDVFEVEKILDMKTEGGKVLYKVRWKGYTSDDDTWEPEIHLEDCKEVLLEFRKK
IAENKAKA

Primary citation

Gluebodies Offer a Route To Improve Crystal Reliability and Diversity through Transferable Nanobody Mutations That Introduce Constitutive Close Contacts. Ye, M., Makola, M., Richards, M.W. et al. ACS Cent Sci (2025) 11:2385-2399. DOI 10.1021/acscentsci.5c00937 · 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
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

About this viewer

MolViewer shows 9H77 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.