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Crystal strucrure of the MPP6 exosome complex

Analyse Crystal strucrure of the MPP6 exosome complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5OKZ
Type: protein
Length: 8,926 residues
Chains: 40
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exosome complex component CSL4; Exosome complex component RRP45; Exosome complex…
UniProt: P53859, Q05636, P46948, P25359, P53256, Q12277, P48240, Q08285, P38792, P53725
Ligands: TAM, MG, CL
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 35 distinct chains · 25% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
m	Exosome complex component CSL4	protein	190	3% helix, 44% strand	P53859
A, K, U, e	Exosome complex component RRP45	protein	295	32% helix, 30% strand	Q05636
B	Exosome complex component SKI6	protein	242	30% helix, 30% strand	P46948
C	Exosome complex component RRP43	protein	313	27% helix, 32% strand	P25359
D	Exosome complex component RRP46	protein	221	34% helix, 37% strand	P53256
E	Exosome complex component RRP42	protein	257	27% helix, 31% strand	Q12277
F	Exosome complex component MTR3	protein	207	29% helix, 35% strand	P48240
G	Exosome complex component RRP40	protein	231	21% helix, 30% strand	Q08285
H	Exosome complex component RRP4	protein	267	27% helix, 31% strand	P38792
I	Exosome complex component CSL4	protein	178	3% helix, 40% strand	P53859
J	M-phase phosphoprotein 6 homolog	protein	20	0% helix, 25% strand	P53725
L	Exosome complex component SKI6	protein	238	30% helix, 31% strand	P46948
M	Exosome complex component RRP43	protein	310	26% helix, 33% strand	P25359
N	Exosome complex component RRP46	protein	222	34% helix, 37% strand	P53256
O	Exosome complex component RRP42	protein	260	27% helix, 32% strand	Q12277
P	Exosome complex component MTR3	protein	208	29% helix, 35% strand	P48240
Q	Exosome complex component RRP40	protein	207	21% helix, 29% strand	Q08285
R	Exosome complex component RRP4	protein	265	25% helix, 33% strand	P38792
S	Exosome complex component CSL4	protein	208	3% helix, 44% strand	P53859
T, d	M-phase phosphoprotein 6 homolog	protein	7	0% helix, 0% strand	P53725
V	Exosome complex component SKI6	protein	241	32% helix, 30% strand	P46948
W	Exosome complex component RRP43	protein	319	26% helix, 32% strand	P25359
X, h	Exosome complex component RRP46	protein	223	34% helix, 37% strand	P53256
Y	Exosome complex component RRP42	protein	263	29% helix, 32% strand	Q12277
Z	Exosome complex component MTR3	protein	208	29% helix, 34% strand	P48240
a	Exosome complex component RRP40	protein	227	20% helix, 29% strand	Q08285
b	Exosome complex component RRP4	protein	262	26% helix, 32% strand	P38792
c	Exosome complex component CSL4	protein	197	3% helix, 43% strand	P53859
f	Exosome complex component SKI6	protein	237	30% helix, 32% strand	P46948
g	Exosome complex component RRP43	protein	317	26% helix, 32% strand	P25359
i	Exosome complex component RRP42	protein	261	29% helix, 31% strand	Q12277
j	Exosome complex component MTR3	protein	206	29% helix, 34% strand	P48240
k	Exosome complex component RRP40	protein	226	21% helix, 31% strand	Q08285
l	Exosome complex component RRP4	protein	268	24% helix, 33% strand	P38792
n	M-phase phosphoprotein 6 homolog	protein	10	0% helix, 40% strand	P53725

Ligands and binding sites

TAM · Tris(hydroxyethyl)aminomethane · ligand · 4 copies · chains A, f, K, U, B, e
MG · Magnesium ion · metal · 2 copies · chains O, R, g
CL · Chloride ion · ion · 7 copies · chains G, H, R, b, f, l

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	1180	0.85	0.86	125	empty
2	1036	0.81	0.82	93	empty
3	925	0.81	0.83	80	empty
4	421	0.80	0.89	54	CL
5	814	0.80	0.83	80	empty

Interfaces

102 interfaces between chains.

e–f · 1883 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 1844 Å² buried · 30 hydrogen bonds · protein-protein
K–L · 1841 Å² buried · 33 hydrogen bonds · protein-protein
U–V · 1833 Å² buried · 29 hydrogen bonds · protein-protein
W–Z · 1724 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

Q12277 · AlphaFold monomer V2.0 prediction for exosome complex component RRP42 (Q12277) · a predicted model of the same protein · chain i against A, TM-score 0.99
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
P38792 · AlphaFold monomer V2.0 prediction for exosome complex component RRP4 (P38792) · a predicted model of the same protein · chain H against A, TM-score 0.99
P46948 · AlphaFold monomer V2.0 prediction for exosome complex component SKI6 (P46948) · a predicted model of the same protein · chain V against A, TM-score 0.98

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 P53859
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 P53725
Elsewhere: RCSB PDB 5OKZ · PDBe 5OKZ · UniProt P53859 · UniProt Q05636 · UniProt P46948 · UniProt P25359 · UniProt P53256 · UniProt Q12277 · UniProt P48240 · UniProt Q08285 · UniProt P38792 · UniProt P53725

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