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Structure of SNF2-nucleosome complex in apo state

Analyse Structure of SNF2-nucleosome complex in apo state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Z3L
Type: protein + DNA
Length: 1,639 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; DNA (167-mer); Transcription…
EC: 3.6.4.-
UniProt: P84233, P62799, Q6AZJ8, P02281, P22082
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 9 distinct chains · 54% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.2	protein	98	66% helix, 3% strand	P84233
B	Histone H4	protein	87	61% helix, 3% strand	P62799
C, G	Histone H2A	protein	107	53% helix, 0% strand	Q6AZJ8
D, H	Histone H2B 1.1	protein	93	71% helix, 0% strand	P02281
E	Histone H3.2	protein	95	68% helix, 3% strand	P84233
F	Histone H4	protein	86	55% helix, 3% strand	P62799
I	DNA (167-mer)	dna	146	—	—
J	DNA (167-mer)	dna	146	—	—
O	Transcription regulatory protein SNF2 (EC 3.6.4.-)	protein	581	47% helix, 7% strand	P22082

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	774	0.86	0.89	89	empty
2	1139	0.82	0.83	102	empty
3	897	0.81	0.83	103	empty
4	127	0.79	0.96	31	empty
5	387	0.77	0.87	56	empty

Interfaces

41 interfaces between chains.

I–J · 6478 Å² buried · 423 hydrogen bonds · nucleic-nucleic
C–D · 2466 Å² buried · 12 hydrogen bonds · protein-protein
G–H · 2444 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 2340 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 2300 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5Z3L · Structure of Snf2-nucleosome complex in apo state · the same entry in another collection · chain O against O, TM-score 1.00
P22082 · AlphaFold monomer V2.0 prediction for transcription regulatory protein SNF2 (P22082) · a predicted model of the same protein · chain O against A, TM-score 0.93

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 P84233
Every structure of UniProt P62799
Every structure of UniProt Q6AZJ8
Every structure of UniProt P02281
Every structure of UniProt P22082
Elsewhere: RCSB PDB 5Z3L · PDBe 5Z3L · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt P22082

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