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Crystal structure of arabidopsis thaliana RNA editing factor MORF1, space group P2(1)

Analyse Crystal structure of arabidopsis thaliana RNA editing factor MORF1, space group… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MPX
Type: protein
Length: 460 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Multiple organellar RNA editing factor 1, mitochondrial
UniProt: O49429
Ligands: SO4
Pockets: 10 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Multiple organellar RNA editing factor 1, mitochondrial	protein	115	28% helix, 31% strand	O49429

Ligands and binding sites

SO4 · Sulfate ion · ion · 7 copies · chains A, D, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	447	0.63	0.77	48	empty
2	209	0.61	0.82	31	empty
3	214	0.60	0.81	31	empty
4	157	0.44	0.75	22	empty
5	58	0.38	0.80	19	empty

Interfaces

6 interfaces between chains.

A–D · 838 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 802 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 796 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 783 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 489 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5MPX · Crystal structure of Arabidopsis thaliana RNA editing factor MORF1, space group P2(1) · the same entry in another collection · chain A against A, TM-score 1.00
O49429 · AlphaFold monomer V2.0 prediction for multiple organellar RNA editing factor 1… · a predicted model of the same protein · chain A against A, TM-score 0.91

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 O49429
Elsewhere: RCSB PDB 5MPX · PDBe 5MPX · UniProt O49429

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