Research workbench

X-ray structure of the mmtv-a nucleosome core particle

Analyse X-ray structure of the mmtv-a nucleosome core particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5F99
Type: protein + DNA
Length: 1,097 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A type 1; Histone H2B 1.1; DNA (147-mer)
UniProt: P84233, P62799, P06897, P02281
Ligands: MG, CL
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 10 distinct chains · 58% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.2	protein	100	63% helix, 3% strand	P84233
B	Histone H4	protein	83	59% helix, 7% strand	P62799
C	Histone H2A type 1	protein	111	53% helix, 6% strand	P06897
D	Histone H2B 1.1	protein	100	69% helix, 4% strand	P02281
E	Histone H3.2	protein	99	64% helix, 4% strand	P84233
F	Histone H4	protein	92	54% helix, 8% strand	P62799
G	Histone H2A type 1	protein	121	40% helix, 6% strand	P06897
H	Histone H2B 1.1	protein	97	70% helix, 4% strand	P02281
I	DNA (147-mer)	dna	147	—	—
J	DNA (147-mer)	dna	147	—	—

Ligands and binding sites

MG · Magnesium ion · metal · chains E, F
CL · Chloride ion · ion · 4 copies · chains A, C, D, J, E, G, H, I

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	767	0.80	0.84	73	empty
2	393	0.77	0.87	50	empty
3	345	0.74	0.86	45	empty
4	1052	0.73	0.76	71	empty
5	177	0.69	0.89	29	empty

Interfaces

38 interfaces between chains.

I–J · 6515 Å² buried · 634 hydrogen bonds · nucleic-nucleic
C–D · 2679 Å² buried · 20 hydrogen bonds · protein-protein
G–H · 2667 Å² buried · 28 hydrogen bonds · protein-protein
E–F · 2662 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 2561 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

5F99 · X-ray Structure of the MMTV-A Nucleosome Core Particle · the same entry in another collection · chain J against J, TM-score 1.00
P06897 · AlphaFold monomer V2.0 prediction for histone H2A type 1 (P06897) · a predicted model of the same protein · chain C against A, TM-score 0.94

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 P84233
Every structure of UniProt P62799
Every structure of UniProt P06897
Every structure of UniProt P02281
Elsewhere: RCSB PDB 5F99 · PDBe 5F99 · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281

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