MolNFT v1 · #160878 · protein + DNA

SET2 bound to nucleosome

6PX1 · Histone H3: “SET2 bound to nucleosome”. Electron microscopy, 20 pockets (best druggability 0.82). MolNFT v1 #160878 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6PX1
Type: protein + DNA
Length: 1,042 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3; Histone H4; Ubiquitin-60S ribosomal protein L40,HISTONE H2A; Histone H2B 1.1…
UniProt: A0A310TTQ1, P62799, P0CH09, Q6AZJ8, P02281
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 6 distinct chains · 61% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Histone H3	protein	98	61% helix, 4% strand	A0A310TTQ1
B, F	Histone H4	protein	80	61% helix, 9% strand	P62799
C, G	Ubiquitin-60S ribosomal protein L40,HISTONE H2A	protein	103	52% helix, 7% strand	P0CH09, Q6AZJ8
D, H	Histone H2B 1.1	protein	95	71% helix, 4% strand	P02281
I	DNA (149-mer)	dna	145	—	—
J	DNA (149-mer)	dna	145	—	—

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1028	0.82	0.83	96	empty
2	355	0.76	0.87	49	empty
3	792	0.72	0.78	55	empty
4	291	0.72	0.86	41	empty
5	876	0.71	0.77	65	empty

Interfaces

38 interfaces between chains.

I–J · 6523 Å² buried · 504 hydrogen bonds · nucleic-nucleic
A–B · 2608 Å² buried · 21 hydrogen bonds · protein-protein
G–H · 2557 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 2536 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 2530 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

6PX1 · Set2 bound to nucleosome · the same entry in another collection · chain J against J, TM-score 1.00
P0CH09 · AlphaFold monomer V2.0 prediction for ubiquitin-60S ribosomal protein L40 (P0CH09) · a predicted model of the same protein · chain C against A, TM-score 0.31

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 A0A310TTQ1
Every structure of UniProt P62799
Every structure of UniProt P0CH09
Every structure of UniProt Q6AZJ8
Every structure of UniProt P02281
Elsewhere: RCSB PDB 6PX1 · PDBe 6PX1 · UniProt A0A310TTQ1 · UniProt P62799 · UniProt P0CH09 · UniProt Q6AZJ8 · UniProt P02281

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