MolNFT v1 · #57925 · protein + DNA

The structure of the centromeric nucleosome containing cenp-a

3AN2 · Histone H3-like centromeric protein a: “The structure of the centromeric nucleosome containing cenp-a”. X-ray diffraction, 20 pockets (best druggability 0.78). MolNFT v1 #57925 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3AN2
Type: protein + DNA
Length: 948 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3-like centromeric protein a; Histone H4; Histone H2A type 1-B/E; Histone H2B…
UniProt: P49450, B2R4R0, P04908, P06899
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 8 distinct chains · 55% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3-like centromeric protein a	protein	89	48% helix, 4% strand	P49450
B	Histone H4	protein	78	59% helix, 8% strand	B2R4R0
C	Histone H2A type 1-B/E	protein	97	55% helix, 4% strand	P04908
D, H	Histone H2B type 1-J	protein	90	62% helix, 3% strand	P06899
E	Histone H3-like centromeric protein a	protein	83	48% helix, 4% strand	P49450
F	Histone H4	protein	79	59% helix, 5% strand	B2R4R0
G	Histone H2A type 1-B/E	protein	100	51% helix, 6% strand	P04908
I, J	147 mer DNA	dna	121	—	—

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	472	0.78	0.86	59	empty
2	346	0.75	0.86	43	empty
3	226	0.73	0.88	41	empty
4	685	0.66	0.75	52	empty
5	143	0.64	0.86	26	empty

Interfaces

38 interfaces between chains.

I–J · 5662 Å² buried · 483 hydrogen bonds · nucleic-nucleic
C–D · 2588 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 2564 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 2460 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 2433 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (engineered).

Compared structures

3AN2 · The structure of the centromeric nucleosome containing CENP-A · the same entry in another collection · chain F against F, TM-score 1.00
P06899 · AlphaFold monomer V2.0 prediction for histone H2B type 1-J (P06899) · a predicted model of the same protein · chain D against A, TM-score 0.97
P49450 · AlphaFold monomer V2.0 prediction for histone H3-like centromeric protein a (P49450) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P49450
Every structure of UniProt B2R4R0
Every structure of UniProt P04908
Every structure of UniProt P06899
Elsewhere: RCSB PDB 3AN2 · PDBe 3AN2 · UniProt P49450 · UniProt B2R4R0 · UniProt P04908 · UniProt P06899

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