Research workbench

Structure of SWI/SNF chromatin remodeler rsc bound to a nucleosome

Analyse Structure of SWI/SNF chromatin remodeler rsc bound to a nucleosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6TDA
Type: protein + DNA
Length: 5,137 residues
Chains: 23
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; DNA-I; DNA-J; Chromatin…
EC: 3.6.4.12
UniProt: P84233, P62799, Q6AZJ8, P02281, Q06168, P43609, P32832, Q03124, P25632, Q07979, Q9URQ5, Q02206, P32597, Q12406, Q05123, P53330
Ligands: ZN
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 21 distinct chains · 45% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.2	protein	96	67% helix, 4% strand	P84233
B	Histone H4	protein	87	57% helix, 8% strand	P62799
C, G	Histone H2A	protein	102	57% helix, 6% strand	Q6AZJ8
D, H	Histone H2B 1.1	protein	92	73% helix, 4% strand	P02281
E	Histone H3.2	protein	95	69% helix, 4% strand	P84233
F	Histone H4	protein	82	62% helix, 7% strand	P62799
I	DNA-I	dna	160	—	—
J	DNA-J	dna	160	—	—
K	Chromatin structure-remodeling complex subunit SFH1	protein	235	40% helix, 14% strand	Q06168
L	Chromatin structure-remodeling complex protein RSC8, chromatin structure-remodeling complex protein RSC8	protein	596	52% helix, 7% strand	P43609
M	Chromatin structure-remodeling complex subunit RSC7	protein	108	32% helix, 19% strand	P32832
N	Chromatin structure-remodeling complex subunit RSC9	protein	367	54% helix, 0% strand	Q03124
O	Chromatin structure-remodeling complex protein RSC6	protein	212	50% helix, 4% strand	P25632
P	Chromatin structure-remodeling complex protein RSC58	protein	347	37% helix, 12% strand	Q07979
Q	High temperature lethal protein 1	protein	58	66% helix, 5% strand	Q9URQ5
R	Chromatin structure-remodeling complex subunit RSC4	protein	131	4% helix, 44% strand	Q02206
S	Nuclear protein STH1/NPS1 (EC 3.6.4.12)	protein	783	52% helix, 8% strand	P32597
T	Actin-related protein 7	protein	399	46% helix, 19% strand	Q12406
U	Actin-like protein ARP9	protein	396	40% helix, 19% strand	Q05123
V	Regulator of TY1 transposition protein 102	protein	54	13% helix, 28% strand	P53330
X	Unknown protein	protein	383	17% helix, 7% strand	—

Ligands and binding sites

ZN · Zinc 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	1121	0.87	0.88	123	empty
2	353	0.84	0.93	45	empty
3	963	0.81	0.82	108	empty
4	760	0.80	0.84	84	empty
5	1043	0.80	0.81	81	empty

Interfaces

76 interfaces between chains.

I–J · 7190 Å² buried · 590 hydrogen bonds · nucleic-nucleic
P–S · 4955 Å² buried · 46 hydrogen bonds · protein-protein
P–X · 4337 Å² buried · 32 hydrogen bonds · protein-protein
L–O · 4078 Å² buried · 32 hydrogen bonds · protein-protein
L–M · 3759 Å² buried · 42 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 modified (engineered).

Compared structures

6TDA · Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome · the same entry in another collection · chain J against J, 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 Q6AZJ8
Every structure of UniProt P02281
Every structure of UniProt Q06168
Every structure of UniProt P43609
Every structure of UniProt P32832
Every structure of UniProt Q03124
Every structure of UniProt P25632
Every structure of UniProt Q07979
Every structure of UniProt Q9URQ5
Every structure of UniProt Q02206
Every structure of UniProt P32597
Every structure of UniProt Q12406
Every structure of UniProt Q05123
Every structure of UniProt P53330
Elsewhere: RCSB PDB 6TDA · PDBe 6TDA · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt Q06168 · UniProt P43609 · UniProt P32832 · UniProt Q03124 · UniProt P25632 · UniProt Q07979 · UniProt Q9URQ5 · UniProt Q02206 · UniProt P32597 · UniProt Q12406 · UniProt Q05123 · UniProt P53330

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