MolNFT v1 · #73711 · protein + DNA

Human MSL3 chromodomain bound to DNA and H4K20ME1 peptide

3OA6 · Male-specific lethal 3 homolog: “Human MSL3 chromodomain bound to DNA and H4K20ME1 peptide”. X-ray diffraction, 4 pockets (best druggability 0.56). MolNFT v1 #73711 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3OA6
Type: protein + DNA
Length: 237 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Male-specific lethal 3 homolog; DNA (5'-D(*GP*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*A)…
UniProt: Q8N5Y2
Pockets: 4 · best druggability 0.56

Structure

x-ray diffraction · 4 distinct chains · 24% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Male-specific lethal 3 homolog	protein	84	25% helix, 40% strand	Q8N5Y2
C, E	DNA (5'-D(GPCPTPAPGPGPTPCPAPAPAPGPGPTPCPA)- 3')	dna	16	—	—
D, F	DNA (5'-D(CPTPGPAPCPCPTPTPTPGPAPCPCPTPAPG)- 3')	dna	16	—	—
G	H4 peptide monomethylated at lysine 20	protein	5	0% helix, 0% strand	—

Ligands and binding sites

IMD · Imidazole · additive · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	412	0.56	0.74	35	empty
2	144	0.50	0.80	23	empty
3	190	0.47	0.75	24	empty
4	166	0.44	0.74	20	IMD

Interfaces

12 interfaces between chains.

E–F · 672 Å² buried · 72 hydrogen bonds · nucleic-nucleic
C–D · 671 Å² buried · 69 hydrogen bonds · nucleic-nucleic
A–G · 397 Å² buried · 2 hydrogen bonds · protein-protein
B–F · 200 Å² buried · 4 hydrogen bonds · protein-nucleic
B–D · 150 Å² buried · 2 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (methylation).

Compared structures

3OA6 · Human MSL3 Chromodomain bound to DNA and H4K20me1 peptide · the same entry in another collection · chain G against G, TM-score 1.00
Q8N5Y2 · AlphaFold monomer V2.0 prediction for male-specific lethal 3 homolog (Q8N5Y2) · a predicted model of the same protein · chain A against A, TM-score 0.95

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q8N5Y2
Elsewhere: RCSB PDB 3OA6 · PDBe 3OA6 · UniProt Q8N5Y2

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