MolNFT v1 · #141329 · protein + DNA

Structure of SNF2-nucleosome complex in ADP state

5Z3O · Histone H3.2: “Structure of SNF2-nucleosome complex in ADP state”. Electron microscopy, 2 ligands (ADP, MG), 20 pockets (best druggability 0.83). MolNFT v1 #141329 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5Z3O
Type: protein + DNA
Length: 1,638 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
Ligands: ADP, MG
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 9 distinct chains · 55% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.2	protein	98	66% helix, 4% strand	P84233
B	Histone H4	protein	87	59% helix, 5% strand	P62799
C, G	Histone H2A	protein	107	53% helix, 2% strand	Q6AZJ8
D, H	Histone H2B 1.1	protein	93	71% helix, 2% strand	P02281
E	Histone H3.2	protein	95	68% helix, 4% strand	P84233
F	Histone H4	protein	86	55% helix, 5% strand	P62799
I	DNA (167-mer)	dna	146	—	—
J	DNA (167-mer)	dna	146	—	—
O	Transcription regulatory protein SNF2 (EC 3.6.4.-)	protein	580	48% helix, 7% strand	P22082

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains O
MG · Magnesium ion · metal · chains O

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	1163	0.83	0.84	116	ADP, MG
2	1027	0.82	0.83	90	empty
3	557	0.78	0.84	75	empty
4	109	0.76	0.96	23	empty
5	1052	0.75	0.78	69	empty

Interfaces

41 interfaces between chains.

I–J · 6417 Å² buried · 397 hydrogen bonds · nucleic-nucleic
C–D · 2518 Å² buried · 16 hydrogen bonds · protein-protein
G–H · 2488 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 2450 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 2418 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

5Z3O · Structure of Snf2-nucleosome complex in ADP 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 5Z3O · PDBe 5Z3O · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt P22082

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