MolNFT v1 · #129893 · protein + DNA

Structure of the 4_601_157 tetranucleosome (C2 form)

5OXV · DNA strand 1 (601-based sequence model): “Structure of the 4_601_157 tetranucleosome (C2 form)”. X-ray diffraction, 20 pockets (best druggability 0.80). MolNFT v1 #129893 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5OXV
Type: protein + DNA
Length: 2,123 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA strand 1 (601-based sequence model); Histone H2B 1.1; Histone H2A; Histone H4…
UniProt: P02281, Q6AZJ8, P62799, P84233
Pockets: 20 · best druggability 0.80

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
J	DNA strand 1 (601-based sequence model)	dna	310	—	—
R, H	Histone H2B 1.1	protein	93	75% helix, 4% strand	P02281
Q, G	Histone H2A	protein	105	54% helix, 7% strand	Q6AZJ8
P, F	Histone H4	protein	78	65% helix, 8% strand	P62799
O, E	Histone H3.2	protein	97	65% helix, 4% strand	P84233
N, D	Histone H2B 1.1	protein	95	74% helix, 4% strand	P02281
M, C	Histone H2A	protein	103	56% helix, 6% strand	Q6AZJ8
L, B	Histone H4	protein	83	60% helix, 8% strand	P62799
K, A	Histone H3.2	protein	97	66% helix, 4% strand	P84233
I	DNA strand 2 (601-based sequence model)	dna	311	—	—

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	638	0.80	0.85	70	empty
2	636	0.79	0.85	75	empty
3	693	0.77	0.82	64	empty
4	485	0.77	0.85	62	empty
5	431	0.76	0.86	48	empty

Interfaces

71 interfaces between chains.

J–I · 14232 Å² buried · 1,487 hydrogen bonds · nucleic-nucleic
D–C · 2692 Å² buried · 30 hydrogen bonds · protein-protein
N–M · 2691 Å² buried · 30 hydrogen bonds · protein-protein
B–A · 2663 Å² buried · 24 hydrogen bonds · protein-protein
L–K · 2662 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

5OXV · Structure of the 4_601_157 tetranucleosome (C2 form) · the same entry in another collection · chain J against J, 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 P02281
Every structure of UniProt Q6AZJ8
Every structure of UniProt P62799
Every structure of UniProt P84233
Elsewhere: RCSB PDB 5OXV · PDBe 5OXV · UniProt P02281 · UniProt Q6AZJ8 · UniProt P62799 · UniProt P84233

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