MolNFT v2 · #216789 · protein + DNA

Cryo-EM structure of NR5A2-nucleosome complex SHL+5.5

8PKI · Histone H3.3: “Cryo-EM structure of NR5A2-nucleosome complex SHL+5.5”. Electron microscopy at 2.58, 1 ligand (ZN), 20 pockets (best druggability 0.79). MolNFT v2 #216789 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 8PKI
Type: protein + DNA
Length: 1,091 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.58
Source: Homo sapiens; Mus musculus; synthetic construct
Molecule: Histone H3.3; Histone H4; Histone H2A; Histone H2B type 1-C/E/G; DNA; Nuclear receptor…
UniProt: P84244, P62806, B2RVF0, Q6ZWY9, O00482
Ligands: ZN
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · resolution 2.58 · 11 distinct chains · 63% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.3	protein	92	72% helix, 4% strand	P84244
B	Histone H4	protein	79	61% helix, 9% strand	P62806
C	Histone H2A	protein	106	53% helix, 7% strand	B2RVF0
D	Histone H2B type 1-C/E/G	protein	91	77% helix, 4% strand	Q6ZWY9
E	Histone H3.3	protein	96	65% helix, 4% strand	P84244
F	Histone H4	protein	78	64% helix, 9% strand	P62806
G	Histone H2A	protein	98	56% helix, 7% strand	B2RVF0
H	Histone H2B type 1-C/E/G	protein	90	78% helix, 4% strand	Q6ZWY9
I	DNA	dna	137	—	—
J	DNA	dna	138	—	—
K	Nuclear receptor subfamily 5 group A member 2	protein	86	42% helix, 7% strand	O00482

Ligands and binding sites

ZN · Zinc ion · metal · chains K

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

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	949	0.79	0.81	90	empty
2	545	0.73	0.82	46	empty
3	500	0.72	0.81	42	empty
4	643	0.66	0.76	41	empty
5	344	0.65	0.81	36	empty

Interfaces

40 interfaces between chains.

I–J · 6139 Å² buried · 473 hydrogen bonds · nucleic-nucleic
C–D · 2643 Å² buried · 17 hydrogen bonds · protein-protein
G–H · 2541 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 2513 Å² buried · 19 hydrogen bonds · protein-protein
E–F · 2496 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

P62806 · AlphaFold monomer V2.0 prediction for histone H4 (P62806) · a predicted model of the same protein · chain F against A, TM-score 0.98
P84244 · AlphaFold monomer V2.0 prediction for histone H3.3 (P84244) · a predicted model of the same protein · chain E against A, TM-score 0.98
O00482 · AlphaFold monomer V2.0 prediction for nuclear receptor subfamily 5 group a member 2… · a predicted model of the same protein · chain K against A, TM-score 0.91
Q6ZWY9 · AlphaFold monomer V2.0 prediction for histone H2B type 1-C/E/G (Q6ZWY9) · a predicted model of the same protein · chain H against A, TM-score 0.89

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 P84244
Every structure of UniProt P62806
Every structure of UniProt B2RVF0
Every structure of UniProt Q6ZWY9
Every structure of UniProt O00482
Elsewhere: RCSB PDB 8PKI · PDBe 8PKI · UniProt P84244 · UniProt P62806 · UniProt B2RVF0 · UniProt Q6ZWY9 · UniProt O00482

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