MolNFT v1 · #166425 · protein + DNA

Structure of a yeast centromeric nucleosome at 2.7 ångström resolution

6UPH · Histone H3-like centromeric protein CSE4: “Structure of a yeast centromeric nucleosome at 2.7 ångström resolution”. Electron microscopy, 20 pockets (best druggability 0.78). MolNFT v1 #166425 on GenesisL1: 3D structure, binding…

PDB: 6UPH
Type: protein + DNA
Length: 970 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3-like centromeric protein CSE4; Histone H4; Histone H2A; Histone H2B.1; DNA…
UniProt: P36012, Q6CMU6, Q6CK59, Q6CK60
Pockets: 20 · best druggability 0.78

Structure

electron microscopy · 9 distinct chains · 63% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3-like centromeric protein CSE4	protein	93	63% helix, 4% strand	P36012
B, F	Histone H4	protein	79	62% helix, 9% strand	Q6CMU6
C	Histone H2A	protein	97	57% helix, 7% strand	Q6CK59
D	Histone H2B.1	protein	96	69% helix, 4% strand	Q6CK60
E	Histone H3-like centromeric protein CSE4	protein	97	64% helix, 4% strand	P36012
G	Histone H2A	protein	99	53% helix, 7% strand	Q6CK59
H	Histone H2B.1	protein	92	74% helix, 4% strand	Q6CK60
I	DNA (119-mer)	dna	119	—	—
J	DNA (119-mer)	dna	119	—	—

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1103	0.78	0.80	114	empty
2	615	0.73	0.81	57	empty
3	399	0.70	0.82	44	empty
4	268	0.68	0.84	26	empty
5	691	0.67	0.76	49	empty

Interfaces

37 interfaces between chains.

I–J · 5469 Å² buried · 475 hydrogen bonds · nucleic-nucleic
A–B · 2650 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 2596 Å² buried · 15 hydrogen bonds · protein-protein
G–H · 2595 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 2583 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

6UPH · Structure of a Yeast Centromeric Nucleosome at 2.7 Angstrom resolution · the same entry in another collection · chain J against J, TM-score 1.00
Q6CK60 · AlphaFold monomer V2.0 prediction for histone H2B.1 (Q6CK60) · a predicted model of the same protein · chain H 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 P36012
Every structure of UniProt Q6CMU6
Every structure of UniProt Q6CK59
Every structure of UniProt Q6CK60
Elsewhere: RCSB PDB 6UPH · PDBe 6UPH · UniProt P36012 · UniProt Q6CMU6 · UniProt Q6CK59 · UniProt Q6CK60

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