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Crystal structure of nucleosome core particle containing a poly (DA.DT) sequence element

Analyse Crystal structure of nucleosome core particle containing a poly (DA.DT)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2FJ7
Type: protein + DNA
Length: 1,052 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 147 bp DNA containing 16 bp poly da element; 147 bp DNA containing 16 bp poly dt element…
UniProt: P62799, P02281
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 8 distinct chains · 59% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I	147 bp DNA containing 16 bp poly da element	dna	147	—	—
J	147 bp DNA containing 16 bp poly dt element	dna	147	—	—
A, E	Histone H3	protein	98	63% helix, 2% strand	—
B	Histone H4	protein	79	57% helix, 4% strand	P62799
C	Histone H2A	protein	107	51% helix, 7% strand	—
D, H	Histone H2B	protein	93	73% helix, 4% strand	P02281
F	Histone H4	protein	84	52% helix, 8% strand	P62799
G	Histone H2A	protein	106	56% helix, 3% strand	—

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	895	0.82	0.84	71	empty
2	429	0.77	0.86	53	empty
3	359	0.73	0.85	40	empty
4	739	0.69	0.76	68	empty
5	558	0.66	0.77	36	empty

Interfaces

36 interfaces between chains.

I–J · 6460 Å² buried · 576 hydrogen bonds · nucleic-nucleic
C–D · 2656 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 2599 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 2538 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 2417 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

2FJ7 · Crystal structure of Nucleosome Core Particle Containing a Poly (dA.dT) Sequence Element · the same entry in another collection · chain I against I, 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 P62799
Every structure of UniProt P02281
Elsewhere: RCSB PDB 2FJ7 · PDBe 2FJ7 · UniProt P62799 · UniProt P02281

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