MolNFT v1 · #166691 · protein + DNA

SWI/SNF nucleosome complex with ADP-befx

6UXW · Histone H3.2: “SWI/SNF nucleosome complex with ADP-befx”. Electron microscopy, 4 ligands (ADP, BEF, MG), 20 pockets (best druggability 0.88). MolNFT v1 #166691 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6UXW
Type: protein + DNA
Length: 4,744 residues
Chains: 28
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A type 1; Histone H2B 1.1; 601 sequence bottom…
EC: 3.6.4.-
UniProt: P84233, P62799, P06897, P02281, Q12406, Q05123, P53330, P22082, P09547, P18480, P32591, P53628, P18888
Ligands: ADP, BEF, MG, PO4
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 25 distinct chains · 52% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
R	Histone H3.2	protein	98	64% helix, 4% strand	P84233
S	Histone H4	protein	82	62% helix, 9% strand	P62799
T, X	Histone H2A type 1	protein	107	55% helix, 7% strand	P06897
U, Y	Histone H2B 1.1	protein	93	74% helix, 4% strand	P02281
V	Histone H3.2	protein	95	66% helix, 4% strand	P84233
W	Histone H4	protein	79	65% helix, 9% strand	P62799
a	601 sequence bottom strand	dna	155	—	—
b	601 sequence top strand	dna	155	—	—
P	Actin-related protein 7	protein	399	46% helix, 19% strand	Q12406
Q	Actin-like protein ARP9	protein	396	40% helix, 19% strand	Q05123
Z	Regulator of TY1 transposition protein 102	protein	54	13% helix, 28% strand	P53330
A	Transcription regulatory protein SNF2 (EC 3.6.4.-)	protein	778	53% helix, 6% strand	P22082
B	SWI/SNF chromatin-remodeling complex subunit SWI1	protein	482	54% helix, 1% strand	P09547
C	SWI/SNF chromatin-remodeling complex subunit SNF5	protein	245	27% helix, 13% strand	P18480
D	SWI/SNF complex subunit SWI3	protein	159	42% helix, 1% strand	P32591
E	SWI/SNF complex subunit SWI3	protein	139	37% helix, 3% strand	P32591
F	SWI/SNF complex subunit SWI3	protein	221	72% helix, 0% strand	P32591
G	SWI/SNF complex subunit SWI3	protein	197	67% helix, 0% strand	P32591
H	Transcription regulatory protein SNF12	protein	257	62% helix, 3% strand	P53628
I	Transcription regulatory protein SNF6	protein	109	51% helix, 0% strand	P18888
J	Unknown protein	protein	67	81% helix, 0% strand	—
K	Unknown protein	protein	28	46% helix, 0% strand	—
L, O	Unknown protein	protein	18	67% helix, 0% strand	—
M	SWI/SNF global transcription activator complex subunit SWP82	protein	83	48% helix, 0% strand	—
N	Unknown protein	protein	30	0% helix, 3% strand	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
BEF · Beryllium trifluoride ion · ligand · chains A
MG · Magnesium ion · metal · chains A
PO4 · Phosphate ion · ion · 12 copies · chains P, Q, A

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	1189	0.88	0.90	138	PO4
2	1109	0.87	0.88	133	empty
3	944	0.87	0.89	140	empty
4	423	0.86	0.93	81	empty
5	869	0.83	0.85	95	empty

Interfaces

97 interfaces between chains.

a–b · 6941 Å² buried · 475 hydrogen bonds · nucleic-nucleic
X–Y · 2574 Å² buried · 17 hydrogen bonds · protein-protein
R–S · 2544 Å² buried · 15 hydrogen bonds · protein-protein
T–U · 2530 Å² buried · 18 hydrogen bonds · protein-protein
V–W · 2482 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6UXW · SWI/SNF nucleosome complex with ADP-BeFx · the same entry in another collection · chain E against E, TM-score 1.00

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 P06897
Every structure of UniProt P02281
Every structure of UniProt Q12406
Every structure of UniProt Q05123
Every structure of UniProt P53330
Every structure of UniProt P22082
Every structure of UniProt P09547
Every structure of UniProt P18480
Every structure of UniProt P32591
Every structure of UniProt P53628
Every structure of UniProt P18888
Elsewhere: RCSB PDB 6UXW · PDBe 6UXW · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281 · UniProt Q12406 · UniProt Q05123 · UniProt P53330 · UniProt P22082 · UniProt P09547 · UniProt P18480 · UniProt P32591 · UniProt P53628 · UniProt P18888

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