MolNFT v1 · #163828 · protein + DNA

CLASS2C : cenp-a nucleosome in complex with cenp-C central region

6SEF · Histone H3-like centromeric protein a: “CLASS2C : cenp-a nucleosome in complex with cenp-C central region”. Electron microscopy, 20 pockets (best druggability 0.81). MolNFT v1 #163828 on GenesisL1: 3D structure, binding sites and…

PDB: 6SEF
Type: protein + DNA
Length: 1,041 residues
Chains: 11
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, Q03188
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 10 distinct chains · 61% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Histone H3-like centromeric protein a	protein	98	65% helix, 4% strand	P49450
B	Histone H4	protein	78	60% helix, 6% strand	P62805
C	Histone H2A type 2-a	protein	96	54% helix, 7% strand	Q6FI13
D	Histone H2B type 1-C/E/F/G/I	protein	92	74% helix, 4% strand	P62807
F	Histone H4	protein	78	63% helix, 9% strand	P62805
G	Histone H2A type 2-a	protein	103	51% helix, 5% strand	Q6FI13
H	Histone H2B type 1-C/E/F/G/I	protein	90	74% helix, 4% strand	P62807
I	DNA (145-mer)	dna	145	—	—
J	DNA (145-mer)	dna	145	—	—
V	Centromere protein C	protein	18	0% helix, 0% strand	Q03188

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	365	0.81	0.90	48	empty
2	102	0.70	0.93	25	empty
3	859	0.70	0.76	51	empty
4	854	0.69	0.75	52	empty
5	78	0.65	0.92	25	empty

Interfaces

43 interfaces between chains.

I–J · 6573 Å² buried · 557 hydrogen bonds · nucleic-nucleic
A–B · 2601 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 2593 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 2544 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 2460 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6SEF · Class2C : CENP-A nucleosome in complex with CENP-C central region · the same entry in another collection · chain V against V, TM-score 1.00
P62805 · AlphaFold monomer V2.0 prediction for histone H4 (P62805) · a predicted model of the same protein · chain F against A, TM-score 0.97

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
Every structure of UniProt Q03188
Elsewhere: RCSB PDB 6SEF · PDBe 6SEF · UniProt P49450 · UniProt P62805 · UniProt Q6FI13 · UniProt P62807 · UniProt Q03188

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.