Research workbench

Yeast mitochondrial RNA degradosome complex mtexo

Analyse Yeast mitochondrial RNA degradosome complex mtexo in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6F4A
Type: protein + RNA
Length: 1,184 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exoribonuclease II, mitochondrial; SUV3 helicase; RNA (5'-R(P*AP*GP*AP*UP*AP*C)-3')
UniProt: A0A0W0CXR7, Q6FKD7
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Exoribonuclease II, mitochondrial	protein	644	46% helix, 11% strand	A0A0W0CXR7
B	SUV3 helicase	protein	534	49% helix, 11% strand	Q6FKD7
C	RNA (5'-R(PAPGPAPUPAPC)-3')	rna	6	—	—

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1032	0.82	0.83	133	empty
2	854	0.80	0.83	103	empty
3	126	0.74	0.93	36	empty
4	681	0.71	0.78	88	empty
5	119	0.70	0.91	32	empty

Interfaces

2 interfaces between chains.

A–B · 1072 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 696 Å² buried · 14 hydrogen bonds · protein-nucleic

Compared structures

6F4A · Yeast mitochondrial RNA degradosome complex mtEXO · the same entry in another collection · chain A against A, 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 A0A0W0CXR7
Every structure of UniProt Q6FKD7
Elsewhere: RCSB PDB 6F4A · PDBe 6F4A · UniProt A0A0W0CXR7 · UniProt Q6FKD7

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