MolNFT v2 · #213126 · protein + DNA

Rpd3S bound to the nucleosome

8IHT · Histone H3: “Rpd3S bound to the nucleosome”. Electron microscopy at 3.72, 2 ligands (ZN, CA), 20 pockets (best druggability 0.81). MolNFT v2 #213126 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 8IHT
Type: protein + DNA
Length: 3,111 residues
Chains: 16
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.72
Source: Saccharomyces cerevisiae; Xenopus laevis
Molecule: Histone H3; Histone H4; Histone H2A; Histone H2B; DNA (164-mer); DNA (165-mer); RCO1…
EC: 3.5.1.98
UniProt: A0A310TTQ1, A0A8J1LTD2, Q6AZJ8, A0A8J0U496, A0A8H4BXB0, A0A8H4F719, P22579, P32561
Ligands: ZN, CA
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · resolution 3.72 · 16 distinct chains · 51% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3	protein	121	49% helix, 2% strand	A0A310TTQ1
B	Histone H4	protein	80	64% helix, 6% strand	A0A8J1LTD2
C	Histone H2A	protein	107	54% helix, 5% strand	Q6AZJ8
D	Histone H2B	protein	94	71% helix, 3% strand	A0A8J0U496
E	Histone H3	protein	100	61% helix, 3% strand	A0A310TTQ1
F	Histone H4	protein	82	63% helix, 6% strand	A0A8J1LTD2
G	Histone H2A	protein	106	56% helix, 6% strand	Q6AZJ8
H	Histone H2B	protein	89	75% helix, 4% strand	A0A8J0U496
I	DNA (164-mer)	dna	158	—	—
J	DNA (165-mer)	dna	159	—	—
M	RCO1 isoform 1	protein	375	21% helix, 11% strand	A0A8H4BXB0
N	Chromatin modification-related protein EAF3	protein	295	54% helix, 13% strand	A0A8H4F719
K	Transcriptional regulatory protein SIN3	protein	598	63% helix, 5% strand	P22579
L	Histone deacetylase RPD3 (EC 3.5.1.98)	protein	410	35% helix, 10% strand	P32561
O	RCO1 isoform 1	protein	153	44% helix, 7% strand	A0A8H4BXB0
P	Chromatin modification-related protein EAF3	protein	184	70% helix, 3% strand	A0A8H4F719

Ligands and binding sites

ZN · Zinc ion · metal · chains L
CA · Calcium ion · metal · chains L

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	946	0.81	0.82	103	empty
2	852	0.80	0.83	97	empty
3	385	0.80	0.89	53	empty
4	584	0.77	0.83	69	empty
5	104	0.77	0.96	25	empty

Interfaces

59 interfaces between chains.

I–J · 7218 Å² buried · 613 hydrogen bonds · nucleic-nucleic
M–K · 3949 Å² buried · 23 hydrogen bonds · protein-protein
K–L · 3602 Å² buried · 32 hydrogen bonds · protein-protein
M–N · 2578 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 2508 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (nonstandard).

Compared structures

P32561 · AlphaFold monomer V2.0 prediction for histone deacetylase RPD3 (P32561) · a predicted model of the same protein · chain L against A, TM-score 0.95
P22579 · AlphaFold monomer V2.0 prediction for transcriptional regulatory protein SIN3 (P22579) · a predicted model of the same protein · chain K against A, TM-score 0.73

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 A0A310TTQ1
Every structure of UniProt A0A8J1LTD2
Every structure of UniProt Q6AZJ8
Every structure of UniProt A0A8J0U496
Every structure of UniProt A0A8H4BXB0
Every structure of UniProt A0A8H4F719
Every structure of UniProt P22579
Every structure of UniProt P32561
Elsewhere: RCSB PDB 8IHT · PDBe 8IHT · UniProt A0A310TTQ1 · UniProt A0A8J1LTD2 · UniProt Q6AZJ8 · UniProt A0A8J0U496 · UniProt A0A8H4BXB0 · UniProt A0A8H4F719 · UniProt P22579 · UniProt P32561

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