MolNFT v1 · #164780 · protein + DNA

Nucleosome with OCT4-SOX2 motif at shl-6

6T93 · Histone H3.1: “Nucleosome with OCT4-SOX2 motif at shl-6”. Electron microscopy, 20 pockets (best druggability 0.77). MolNFT v1 #164780 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6T93
Type: protein + DNA
Length: 1,060 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.1; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; DNA (153-mer)
UniProt: P68431, P62805, P04908, P06899
Pockets: 20 · best druggability 0.77

Structure

electron microscopy · 6 distinct chains · 63% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Histone H3.1	protein	96	65% helix, 4% strand	P68431
B, F	Histone H4	protein	81	59% helix, 7% strand	P62805
C, G	Histone H2A type 1-B/E	protein	108	53% helix, 6% strand	P04908
D, H	Histone H2B type 1-J	protein	94	74% helix, 4% strand	P06899
I	DNA (153-mer)	dna	151	—	—
J	DNA (153-mer)	dna	151	—	—

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	837	0.77	0.81	80	empty
2	463	0.76	0.85	43	empty
3	423	0.74	0.84	42	empty
4	252	0.71	0.87	35	empty
5	935	0.70	0.75	58	empty

Interfaces

36 interfaces between chains.

I–J · 6763 Å² buried · 542 hydrogen bonds · nucleic-nucleic
C–D · 2542 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 2541 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 2538 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 2531 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

6T93 · Nucleosome with OCT4-SOX2 motif at SHL-6 · the same entry in another collection · chain H against H, TM-score 1.00
P68431 · AlphaFold monomer V2.0 prediction for histone H3.1 (P68431) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P68431
Every structure of UniProt P62805
Every structure of UniProt P04908
Every structure of UniProt P06899
Elsewhere: RCSB PDB 6T93 · PDBe 6T93 · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899

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