MolNFT v1 · #129904 · protein + DNA

Structure of the 4_601_157 tetranucleosome (P1 form)

5OY7 · Histone H2B 1.1: “Structure of the 4_601_157 tetranucleosome (P1 form)”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.79). MolNFT v1 #129904 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5OY7
Type: protein + DNA
Length: 4,241 residues
Chains: 34
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H2B 1.1; Histone H3; Histone H4; Histone H2A; DNA (619-mer)
UniProt: P02281, Q92133, P62799, Q6AZJ8
Ligands: CL
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 11 distinct chains · 63% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, D, T, b	Histone H2B 1.1	protein	95	74% helix, 4% strand	P02281
M, E, U, c	Histone H3	protein	97	65% helix, 4% strand	Q92133
N, F, V, d	Histone H4	protein	78	65% helix, 8% strand	P62799
O, G, W, e	Histone H2A	protein	105	54% helix, 7% strand	Q6AZJ8
P, H, X, f	Histone H2B 1.1	protein	93	75% helix, 4% strand	P02281
Q, I, A, Y	Histone H3	protein	97	66% helix, 4% strand	Q92133
R	Histone H4	protein	82	55% helix, 9% strand	P62799
J, B, Z	Histone H4	protein	83	60% helix, 8% strand	P62799
C, K, S, a	Histone H2A	protein	103	56% helix, 6% strand	Q6AZJ8
g	DNA (619-mer)	dna	619	—	—
h	DNA (619-mer)	dna	619	—	—

Ligands and binding sites

CL · Chloride ion · ion · 8 copies · chains O, P, g, C, D, h, G, H, L, K, S, T, W, X, a, b, e, f

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

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	768	0.79	0.83	76	empty
2	514	0.78	0.85	60	empty
3	487	0.77	0.85	56	empty
4	650	0.77	0.83	67	empty
5	618	0.77	0.83	66	empty

Interfaces

141 interfaces between chains.

g–h · 28265 Å² buried · 2,948 hydrogen bonds · nucleic-nucleic
a–b · 2695 Å² buried · 30 hydrogen bonds · protein-protein
S–T · 2693 Å² buried · 30 hydrogen bonds · protein-protein
L–K · 2692 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 2688 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

5OY7 · Structure of the 4_601_157 tetranucleosome (P1 form) · the same entry in another collection · chain L against L, 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 Q92133
Every structure of UniProt P62799
Every structure of UniProt Q6AZJ8
Elsewhere: RCSB PDB 5OY7 · PDBe 5OY7 · UniProt P02281 · UniProt Q92133 · UniProt P62799 · UniProt Q6AZJ8

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