MolNFT v1 · #163813 · protein + DNA

Class 1 : cenp-a nucleosome

6SE0 · Histone H3-like centromeric protein a: “Class 1 : cenp-a nucleosome”. Electron microscopy, 20 pockets (best druggability 0.80). MolNFT v1 #163813 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6SE0
Type: protein + DNA
Length: 1,055 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3-like centromeric protein a; Histone H4; Histone H2A type 2-a; Histone H2B type…
UniProt: P49450, P62805, Q6FI13, P62807
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 8 distinct chains · 62% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Histone H3-like centromeric protein a	protein	99	66% helix, 4% strand	P49450
B, F	Histone H4	protein	80	63% helix, 6% strand	P62805
C	Histone H2A type 2-a	protein	110	52% helix, 6% strand	Q6FI13
D	Histone H2B type 1-C/E/F/G/I	protein	95	71% helix, 4% strand	P62807
G	Histone H2A type 2-a	protein	108	54% helix, 5% strand	Q6FI13
H	Histone H2B type 1-C/E/F/G/I	protein	94	71% helix, 4% strand	P62807
I	DNA (145-mer)	dna	145	—	—
J	DNA (145-mer)	dna	145	—	—

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	376	0.80	0.89	42	empty
2	178	0.75	0.92	40	empty
3	200	0.74	0.90	45	empty
4	1165	0.72	0.76	73	empty
5	1032	0.72	0.76	56	empty

Interfaces

39 interfaces between chains.

I–J · 6480 Å² buried · 544 hydrogen bonds · nucleic-nucleic
G–H · 2734 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2677 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 2644 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 2571 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6SE0 · Class 1 : CENP-A nucleosome · the same entry in another collection · chain J against J, TM-score 1.00
P49450 · AlphaFold monomer V2.0 prediction for histone H3-like centromeric protein a (P49450) · a predicted model of the same protein · chain E against A, TM-score 0.95

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 P62805
Every structure of UniProt Q6FI13
Every structure of UniProt P62807
Elsewhere: RCSB PDB 6SE0 · PDBe 6SE0 · UniProt P49450 · UniProt P62805 · UniProt Q6FI13 · UniProt P62807

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