MolNFT v1 · #115633 · protein + DNA

Nucleosome containing unmethylated SAT2R DNA

5CPI · Histone H3.1: “Nucleosome containing unmethylated SAT2R DNA”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #115633 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5CPI
Type: protein + DNA
Length: 1,044 residues
Chains: 10
Method: x-ray diffraction
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 (146-mer)
UniProt: P68431, P62805, P04908, P06899
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 10 distinct chains · 64% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.1	protein	97	65% helix, 4% strand	P68431
B	Histone H4	protein	78	64% helix, 9% strand	P62805
C	Histone H2A type 1-B/E	protein	108	55% helix, 6% strand	P04908
D	Histone H2B type 1-J	protein	93	74% helix, 4% strand	P06899
E	Histone H3.1	protein	98	63% helix, 4% strand	P68431
F	Histone H4	protein	83	60% helix, 8% strand	P62805
G	Histone H2A type 1-B/E	protein	104	57% helix, 7% strand	P04908
H	Histone H2B type 1-J	protein	91	76% helix, 4% strand	P06899
I	DNA (146-mer)	dna	146	—	—
J	DNA (146-mer)	dna	146	—	—

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	818	0.81	0.84	68	empty
2	458	0.79	0.87	57	empty
3	452	0.78	0.86	45	empty
4	832	0.74	0.79	67	empty
5	636	0.72	0.79	53	empty

Interfaces

38 interfaces between chains.

I–J · 6375 Å² buried · 615 hydrogen bonds · nucleic-nucleic
E–F · 2658 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 2646 Å² buried · 28 hydrogen bonds · protein-protein
G–H · 2562 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2481 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

5CPI · Nucleosome containing unmethylated Sat2R DNA · the same entry in another collection · chain A against A, TM-score 1.00

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 5CPI · PDBe 5CPI · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899

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