MolNFT v1 · #115635 · protein + DNA

Nucleosome containing methylated SAT2L DNA

5CPK · Histone H3.1: “Nucleosome containing methylated SAT2L DNA”. X-ray diffraction, 20 pockets (best druggability 0.75). MolNFT v1 #115635 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5CPK
Type: protein + DNA
Length: 1,040 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 (145-mer)
UniProt: P68431, P62805, P04908, P06899
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 10 distinct chains · 65% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.1	protein	97	64% helix, 4% strand	P68431
B	Histone H4	protein	79	62% helix, 9% strand	P62805
C	Histone H2A type 1-B/E	protein	106	56% helix, 7% strand	P04908
D	Histone H2B type 1-J	protein	92	75% helix, 4% strand	P06899
E	Histone H3.1	protein	98	65% helix, 4% strand	P68431
F	Histone H4	protein	83	61% helix, 8% strand	P62805
G	Histone H2A type 1-B/E	protein	104	59% helix, 7% strand	P04908
H	Histone H2B type 1-J	protein	91	76% helix, 4% strand	P06899
I	DNA (145-mer)	dna	145	—	—
J	DNA (145-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	386	0.75	0.86	49	empty
2	458	0.75	0.84	48	empty
3	442	0.74	0.83	56	empty
4	219	0.69	0.87	33	empty
5	774	0.68	0.76	65	empty

Interfaces

36 interfaces between chains.

I–J · 6405 Å² buried · 570 hydrogen bonds · nucleic-nucleic
E–F · 2666 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 2579 Å² buried · 24 hydrogen bonds · protein-protein
G–H · 2538 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 2484 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (nucleotide modification).

Compared structures

5CPK · Nucleosome containing methylated Sat2L 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 5CPK · PDBe 5CPK · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899

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