MolNFT v1 · #137796 · protein + RNA

Structure of a twelve component MPP6-nuclear RNA exosome complex bound to RNA

5VZJ · Exosome complex component RRP45: “Structure of a twelve component MPP6-nuclear RNA exosome complex bound to RNA”. X-ray diffraction, 2 ligands (ZN, SO4), 20 pockets (best druggability 0.84). MolNFT v1 #137796 on GenesisL1: 3D…

PDB: 5VZJ
Type: protein + RNA
Length: 3,719 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, Q12149, Q08162, P53725
Ligands: ZN, SO4
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 14 distinct chains · 29% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Exosome complex component RRP45	protein	302	30% helix, 30% strand	Q05636
B	Exosome complex component SKI6	protein	241	29% helix, 31% strand	P46948
C	Exosome complex component RRP43	protein	299	27% helix, 32% strand	P25359
D	Exosome complex component RRP46	protein	222	32% helix, 37% strand	P53256
E	Exosome complex component RRP42	protein	257	24% helix, 33% strand	Q12277
F	Exosome complex component MTR3	protein	207	28% helix, 38% strand	P48240
G	Exosome complex component RRP40	protein	236	18% helix, 32% strand	Q08285
H	Exosome complex component RRP4	protein	291	22% helix, 30% strand	P38792
I	Exosome complex component CSL4	protein	207	9% helix, 36% strand	P53859
J	Exosome complex exonuclease RRP6 (EC 3.1.13.-)	protein	460	42% helix, 10% strand	Q12149
K	Exosome complex exonuclease DIS3 (EC 3.1.13.-, 3.1.26.-)	protein	956	33% helix, 24% strand	Q08162
L	M-phase phosphoprotein 6 homolog	protein	29	0% helix, 14% strand	P53725
M	RNA (11-mer)	rna	5	—	—
N	RNA (19-mer)	rna	7	—	—

Ligands and binding sites

ZN · Zinc ion · metal · chains K
SO4 · Sulfate ion · ion · 5 copies · chains A, B, G, K
GOL · Glycerol · additive · 2 copies · chains A, K

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	790	0.84	0.87	77	empty
2	1075	0.80	0.81	91	empty
3	690	0.80	0.84	75	empty
4	786	0.79	0.83	93	SO4
5	880	0.79	0.82	65	empty

Interfaces

36 interfaces between chains.

A–B · 1876 Å² buried · 29 hydrogen bonds · protein-protein
C–F · 1825 Å² buried · 17 hydrogen bonds · protein-protein
E–H · 1799 Å² buried · 26 hydrogen bonds · protein-protein
B–K · 1697 Å² buried · 33 hydrogen bonds · protein-protein
H–J · 1641 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5VZJ · Structure of a twelve component MPP6-nuclear RNA exosome complex bound to RNA · 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 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
Every structure of UniProt P53725
Elsewhere: RCSB PDB 5VZJ · PDBe 5VZJ · UniProt Q05636 · UniProt P46948 · UniProt P25359 · UniProt P53256 · UniProt Q12277 · UniProt P48240 · UniProt Q08285 · UniProt P38792 · UniProt P53859 · UniProt Q12149 · UniProt Q08162 · UniProt P53725

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