MolNFT v1 · #102508 · protein + RNA

Structure of an RRP6-RNA exosome complex bound to POLY(A) RNA

4OO1 · Exosome complex component RRP45: “Structure of an RRP6-RNA exosome complex bound to POLY(A) RNA”. X-ray diffraction, 2 ligands (MG, PO4), 20 pockets (best druggability 0.80). MolNFT v1 #102508 on GenesisL1: 3D structure, binding…

PDB: 4OO1
Type: protein + RNA
Length: 2,747 residues
Chains: 11
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.-
UniProt: Q05636, P46948, P25359, P53256, Q12277, P48240, Q08285, P38792, P53859, Q12149
Ligands: MG, PO4
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 11 distinct chains · 28% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Exosome complex component RRP45	protein	293	31% helix, 29% strand	Q05636
B	Exosome complex component SKI6	protein	239	28% helix, 30% strand	P46948
C	Exosome complex component RRP43	protein	312	24% helix, 33% strand	P25359
D	Exosome complex component RRP46	protein	221	36% helix, 37% strand	P53256
E	Exosome complex component RRP42	protein	255	25% helix, 32% strand	Q12277
F	Exosome complex component MTR3 (EC 3.1.13.-)	protein	207	31% helix, 35% strand	P48240
G	Exosome complex component RRP40	protein	226	21% helix, 27% strand	Q08285
H	Exosome complex component RRP4	protein	279	27% helix, 30% strand	P38792
I	Exosome complex component CSL4	protein	216	4% helix, 48% strand	P53859
J	Exosome complex exonuclease RRP6 (EC 3.1.13.-)	protein	493	37% helix, 10% strand	Q12149
S	Poly a RNA	rna	6	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains B, E, J, S
PO4 · Phosphate ion · ion · 2 copies · chains I, G, S
MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains E
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, G

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	807	0.80	0.83	71	empty
2	762	0.78	0.82	81	empty
3	1036	0.77	0.79	83	empty
4	515	0.76	0.84	73	empty
5	598	0.75	0.82	56	empty

Interfaces

29 interfaces between chains.

C–J · 1899 Å² buried · 24 hydrogen bonds · protein-protein
C–F · 1817 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1624 Å² buried · 22 hydrogen bonds · protein-protein
E–H · 1611 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1538 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

4OO1 · Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA · the same entry in another collection · chain S against S, TM-score 1.00
P53256 · AlphaFold monomer V2.0 prediction for exosome complex component RRP46 (P53256) · a predicted model of the same protein · chain D against A, TM-score 0.99

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
Elsewhere: RCSB PDB 4OO1 · PDBe 4OO1 · UniProt Q05636 · UniProt P46948 · UniProt P25359 · UniProt P53256 · UniProt Q12277 · UniProt P48240 · UniProt Q08285 · UniProt P38792 · UniProt P53859 · UniProt Q12149

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