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Archaeal exosome core

Analyse Archaeal exosome core in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2BA0
Type: protein
Length: 2,154 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Archaeal exosome RNA binding protein RRP4; Archaeal exosome RNA binding protein RRP41…
EC: 3.1.13.-
UniProt: O29758, O29757, O29756
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 7 distinct chains · 30% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Archaeal exosome RNA binding protein RRP4	protein	218	26% helix, 33% strand	O29758
B	Archaeal exosome RNA binding protein RRP4	protein	222	27% helix, 32% strand	O29758
F	Archaeal exosome RNA binding protein RRP41 (EC 3.1.13.-)	protein	246	33% helix, 35% strand	O29757
E, D	Archaeal exosome RNA binding protein RRP41 (EC 3.1.13.-)	protein	243	33% helix, 34% strand	O29757
I	Archaeal exosome RNA binding protein RRP42 (EC 3.1.13.-)	protein	253	31% helix, 30% strand	O29756
H	Archaeal exosome RNA binding protein RRP42 (EC 3.1.13.-)	protein	256	30% helix, 31% strand	O29756
G	Archaeal exosome RNA binding protein RRP42 (EC 3.1.13.-)	protein	255	27% helix, 31% strand	O29756

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	864	0.82	0.84	87	empty
2	793	0.78	0.82	74	empty
3	1047	0.78	0.80	87	empty
4	433	0.75	0.84	63	empty
5	662	0.74	0.80	67	empty

Interfaces

15 interfaces between chains.

A–D · 1772 Å² buried · 25 hydrogen bonds · protein-protein
C–F · 1767 Å² buried · 23 hydrogen bonds · protein-protein
B–E · 1654 Å² buried · 21 hydrogen bonds · protein-protein
D–G · 1619 Å² buried · 35 hydrogen bonds · protein-protein
E–H · 1576 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

2BA0 · Archaeal exosome core · the same entry in another collection · chain G against G, TM-score 1.00
O29756 · AlphaFold monomer V2.0 prediction for exosome complex component RRP42 (O29756) · a predicted model of the same protein · chain I 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 O29758
Every structure of UniProt O29757
Every structure of UniProt O29756
Elsewhere: RCSB PDB 2BA0 · PDBe 2BA0 · UniProt O29758 · UniProt O29757 · UniProt O29756

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