MolNFT v1 · #187799 · protein + DNA

2.6 a structure of a 40-601[TA-RICH+1]-40 nucleosome

7SWY · Histone H3: “2.6 a structure of a 40-601[TA-RICH+1]-40 nucleosome”. Electron microscopy, 20 pockets (best druggability 0.79). MolNFT v1 #187799 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7SWY
Type: protein + DNA
Length: 1,037 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3; Histone H4; Histone H2A; Histone H2B; DNA tracking strand; DNA guide strand
UniProt: A0A310TTQ1, P62799, P06897, A0A1L8FQ56
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 10 distinct chains · 62% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3	protein	95	61% helix, 4% strand	A0A310TTQ1
B	Histone H4	protein	83	58% helix, 8% strand	P62799
C	Histone H2A	protein	105	53% helix, 7% strand	P06897
D	Histone H2B	protein	96	71% helix, 4% strand	A0A1L8FQ56
E	Histone H3	protein	97	65% helix, 4% strand	A0A310TTQ1
F	Histone H4	protein	85	56% helix, 8% strand	P62799
G	Histone H2A	protein	98	56% helix, 7% strand	P06897
H	Histone H2B	protein	92	74% helix, 4% strand	A0A1L8FQ56
I	DNA tracking strand	dna	143	—	—
J	DNA guide strand	dna	143	—	—

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	1032	0.79	0.81	83	empty
2	600	0.74	0.81	55	empty
3	276	0.71	0.86	32	empty
4	338	0.71	0.84	39	empty
5	262	0.67	0.84	36	empty

Interfaces

34 interfaces between chains.

I–J · 6500 Å² buried · 511 hydrogen bonds · nucleic-nucleic
E–F · 2638 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 2585 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 2583 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 2509 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

7SWY · 2.6 A structure of a 40-601[TA-rich+1]-40 nucleosome · the same entry in another collection · chain J against J, TM-score 1.00
P62799 · AlphaFold monomer V2.0 prediction for histone H4 (P62799) · a predicted model of the same protein · chain B against A, TM-score 0.97
P06897 · AlphaFold monomer V2.0 prediction for histone H2A type 1 (P06897) · a predicted model of the same protein · chain G against A, TM-score 0.96

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 P06897
Every structure of UniProt A0A1L8FQ56
Elsewhere: RCSB PDB 7SWY · PDBe 7SWY · UniProt A0A310TTQ1 · UniProt P62799 · UniProt P06897 · UniProt A0A1L8FQ56

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