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Structure of a 12-subunit nuclear exosome complex bound to single- stranded RNA substrates

Analyse Structure of a 12-subunit nuclear exosome complex bound to single- stranded RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5C0W
Type: protein + RNA
Length: 3,993 residues
Chains: 14
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, Q08162, Q12149, P38801
Ligands: MG, ZN
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 14 distinct chains · 33% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Exosome complex component RRP45	protein	298	30% helix, 31% strand	Q05636
B	Exosome complex component SKI6	protein	244	29% helix, 29% strand	P46948
C	Exosome complex component RRP43	protein	321	27% helix, 30% strand	P25359
D	Exosome complex component RRP46	protein	222	33% helix, 36% strand	P53256
E	Exosome complex component RRP42	protein	266	26% helix, 32% strand	Q12277
F	Exosome complex component MTR3	protein	213	31% helix, 34% strand	P48240
G	Exosome complex component RRP40	protein	236	21% helix, 29% strand	Q08285
H	Exosome complex component RRP4	protein	291	25% helix, 29% strand	P38792
I	Exosome complex component CSL4	protein	225	4% helix, 44% strand	P53859
J	Exosome complex exonuclease DIS3 (EC 3.1.13.-, 3.1.26.-)	protein	970	34% helix, 25% strand	Q08162
K	Exosome complex exonuclease RRP6 (EC 3.1.13.-)	protein	576	52% helix, 7% strand	Q12149
L	Exosome complex protein LRP1	protein	113	86% helix, 0% strand	P38801
R	RNA synthetic	rna	12	—	—
N	RNA synthetic	rna	6	—	—

Ligands and binding sites

MG · Magnesium ion · metal · chains J, R
ZN · Zinc ion · metal · chains J

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	1018	0.84	0.85	114	empty
2	320	0.80	0.91	44	empty
3	392	0.80	0.89	51	empty
4	954	0.80	0.82	82	empty
5	881	0.79	0.82	101	empty

Interfaces

36 interfaces between chains.

K–L · 2759 Å² buried · 3 hydrogen bonds · protein-protein
E–H · 1799 Å² buried · 29 hydrogen bonds · protein-protein
C–F · 1682 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1571 Å² buried · 23 hydrogen bonds · protein-protein
B–J · 1537 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

5C0W · Structure of a 12-subunit nuclear exosome complex bound to single-stranded RNA substrates · the same entry in another collection · chain K against K, 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 Q08162
Every structure of UniProt Q12149
Every structure of UniProt P38801
Elsewhere: RCSB PDB 5C0W · PDBe 5C0W · UniProt Q05636 · UniProt P46948 · UniProt P25359 · UniProt P53256 · UniProt Q12277 · UniProt P48240 · UniProt Q08285 · UniProt P38792 · UniProt P53859 · UniProt Q08162 · UniProt Q12149 · UniProt P38801

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