MolNFT v1 · #160880 · protein + DNA

SET2 bound to nucleosome

6PX3 · Histone H3: “SET2 bound to nucleosome”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.83). MolNFT v1 #160880 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6PX3
Type: protein + DNA
Length: 1,349 residues
Chains: 11
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…
EC: 2.1.1.43
UniProt: A0A310TTQ1, P62799, P0CH09, Q6AZJ8, P02281, G0S676
Ligands: ZN
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 11 distinct chains · 50% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3	protein	96	67% helix, 4% strand	A0A310TTQ1
B	Histone H4	protein	78	65% helix, 9% strand	P62799
C	Ubiquitin-60S ribosomal protein L40,HISTONE H2A	protein	179	44% helix, 18% strand	P0CH09, Q6AZJ8
D	Histone H2B 1.1	protein	96	71% helix, 4% strand	P02281
E	Histone H3	protein	102	63% helix, 6% strand	A0A310TTQ1
F	Histone H4	protein	78	64% helix, 9% strand	P62799
G	Ubiquitin-60S ribosomal protein L40,HISTONE H2A	protein	103	56% helix, 7% strand	P0CH09, Q6AZJ8
H	Histone H2B 1.1	protein	94	73% helix, 4% strand	P02281
I	DNA (145-mer)	dna	145	—	—
J	DNA (145-mer)	dna	145	—	—
S	Histone-lysine N-methyltransferase (EC 2.1.1.43)	protein	233	10% helix, 21% strand	G0S676

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains S

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

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	623	0.83	0.88	67	empty
2	1089	0.74	0.77	72	empty
3	234	0.73	0.88	35	empty
4	449	0.71	0.82	58	empty
5	222	0.71	0.87	38	empty

Interfaces

40 interfaces between chains.

I–J · 6524 Å² buried · 548 hydrogen bonds · nucleic-nucleic
C–D · 3026 Å² buried · 27 hydrogen bonds · protein-protein
G–H · 2625 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 2508 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 2491 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6PX3 · Set2 bound to nucleosome · the same entry in another collection · chain S against S, 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 0.42

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
Every structure of UniProt G0S676
Elsewhere: RCSB PDB 6PX3 · PDBe 6PX3 · UniProt A0A310TTQ1 · UniProt P62799 · UniProt P0CH09 · UniProt Q6AZJ8 · UniProt P02281 · UniProt G0S676

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