MolNFT v1 · #123251 · protein + RNA

Structure of a cytoplasmic 11-subunit RNA exosome complex including SKI7, bound to RNA

5JEA · Exosome complex component RRP45: “Structure of a cytoplasmic 11-subunit RNA exosome complex including SKI7, bound to RNA”. X-ray diffraction, 2 ligands (NA, ZN), 20 pockets (best druggability 0.86). MolNFT v1 #123251 on GenesisL1…

PDB: 5JEA
Type: protein + RNA
Length: 3,445 residues
Chains: 12
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.-, 3.2.1.17
UniProt: Q05636, P46948, P25359, P53256, Q12277, P48240, Q08285, P38792, P53859, Q08162, Q08491, P00720
Ligands: NA, ZN
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 12 distinct chains · 29% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Exosome complex component RRP45	protein	299	31% helix, 30% strand	Q05636
B	Exosome complex component SKI6	protein	243	29% helix, 30% strand	P46948
C	Exosome complex component RRP43	protein	314	26% helix, 33% strand	P25359
D	Exosome complex component RRP46	protein	224	34% helix, 36% strand	P53256
E	Exosome complex component RRP42	protein	256	26% helix, 32% strand	Q12277
F	Exosome complex component MTR3	protein	210	32% helix, 35% strand	P48240
G	Exosome complex component RRP40	protein	235	17% helix, 29% strand	Q08285
H	Exosome complex component RRP4	protein	282	27% helix, 30% strand	P38792
I	Exosome complex component CSL4	protein	235	6% helix, 42% strand	P53859
J	Exosome complex exonuclease DIS3 (EC 3.1.13.-, 3.1.26.-)	protein	936	32% helix, 25% strand	Q08162
K	Superkiller protein 7,ENDOLYSIN (EC 3.2.1.17)	protein	185	56% helix, 1% strand	Q08491, P00720
R	RNA (29-mer)	rna	26	—	—

Ligands and binding sites

NA · Sodium ion · metal · 4 copies · chains B, F, J
ZN · Zinc ion · metal · chains J
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 7 copies · chains A, C, D, G, B, 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	483	0.86	0.93	61	MPD
2	1063	0.85	0.86	90	empty
3	679	0.82	0.87	78	empty
4	491	0.82	0.89	85	empty
5	1138	0.78	0.80	92	empty

Interfaces

34 interfaces between chains.

A–B · 1905 Å² buried · 35 hydrogen bonds · protein-protein
F–I · 1717 Å² buried · 16 hydrogen bonds · protein-protein
I–K · 1711 Å² buried · 18 hydrogen bonds · protein-protein
C–F · 1664 Å² buried · 10 hydrogen bonds · protein-protein
J–R · 1632 Å² buried · 51 hydrogen bonds · protein-nucleic

Compared structures

5JEA · Structure of a cytoplasmic 11-subunit RNA exosome complex including Ski7, bound to RNA · the same entry in another collection · chain R against R, 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 Q08491
Every structure of UniProt P00720
Elsewhere: RCSB PDB 5JEA · PDBe 5JEA · UniProt Q05636 · UniProt P46948 · UniProt P25359 · UniProt P53256 · UniProt Q12277 · UniProt P48240 · UniProt Q08285 · UniProt P38792 · UniProt P53859 · UniProt Q08162 · UniProt Q08491 · UniProt P00720

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.