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Structure of an eleven component nuclear RNA exosome complex bound to RNA

Analyse Structure of an eleven component nuclear RNA exosome complex bound to RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5K36
Type: protein + RNA
Length: 3,755 residues
Chains: 13
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exosome complex component RRP45; Exosome complex component SKI6; Exosome complex…
EC: 3.1.13.-, 3.1.26.-
UniProt: Q05636, P46948, P25359, P53256, Q12277, P48240, Q08285, P38792, P53859, Q12149, Q08162
Ligands: ZN, SO4
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 13 distinct chains · 29% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Exosome complex component RRP45	protein	290	31% helix, 33% strand	Q05636
B	Exosome complex component SKI6	protein	239	31% helix, 31% strand	P46948
C	Exosome complex component RRP43	protein	340	28% helix, 31% strand	P25359
D	Exosome complex component RRP46	protein	221	34% helix, 37% strand	P53256
E	Exosome complex component RRP42	protein	259	25% helix, 34% strand	Q12277
F	Exosome complex component MTR3	protein	215	27% helix, 34% strand	P48240
G	Exosome complex component RRP40	protein	232	19% helix, 31% strand	Q08285
H	Exosome complex component RRP4	protein	289	24% helix, 31% strand	P38792
I	Exosome complex component CSL4	protein	224	8% helix, 47% strand	P53859
J	Exosome complex exonuclease RRP6 (EC 3.1.13.-)	protein	467	43% helix, 9% strand	Q12149
K	Exosome complex exonuclease DIS3 (EC 3.1.13.-, 3.1.26.-)	protein	955	32% helix, 26% strand	Q08162
M	RNA (17-mer)	rna	7	—	—
L	RNA (17-mer)	rna	17	—	—

Ligands and binding sites

ZN · Zinc ion · metal · chains K
SO4 · Sulfate ion · ion · 10 copies · chains A, B, E, D, C, F, G, I, K, M
GOL · Glycerol · additive · 7 copies · chains A, K, C, B, H, J, M

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	376	0.84	0.93	41	empty
2	987	0.84	0.85	102	empty
3	1118	0.82	0.83	70	empty
4	514	0.81	0.88	63	GOL
5	722	0.81	0.85	85	empty

Interfaces

38 interfaces between chains.

C–F · 2017 Å² buried · 28 hydrogen bonds · protein-protein
E–H · 1842 Å² buried · 31 hydrogen bonds · protein-protein
B–K · 1680 Å² buried · 29 hydrogen bonds · protein-protein
A–K · 1635 Å² buried · 29 hydrogen bonds · protein-protein
C–J · 1573 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5K36 · Structure of an eleven component nuclear RNA exosome complex bound to RNA · the same entry in another collection · chain L against L, 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 Q05636
Every structure of UniProt P46948
Every structure of UniProt P25359
Every structure of UniProt P53256
Every structure of UniProt Q12277
Every structure of UniProt P48240
Every structure of UniProt Q08285
Every structure of UniProt P38792
Every structure of UniProt P53859
Every structure of UniProt Q12149
Every structure of UniProt Q08162
Elsewhere: RCSB PDB 5K36 · PDBe 5K36 · UniProt Q05636 · UniProt P46948 · UniProt P25359 · UniProt P53256 · UniProt Q12277 · UniProt P48240 · UniProt Q08285 · UniProt P38792 · UniProt P53859 · UniProt Q12149 · UniProt Q08162

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