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MS2-RNA hairpin (C-10) complex

Analyse MS2-RNA hairpin (C-10) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2IZM
Type: protein + RNA
Length: 413 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MS2 coat protein; 5'-R(*AP*CP*AP*UP*GP*CP*GP*GP*AP*UP *CP*AP*CP*CP*CP*AP*UP*GP*U)-3'
UniProt: P03612
Pockets: 5 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 19% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	MS2 coat protein	protein	129	19% helix, 46% strand	P03612
R, S	5'-R(APCPAPUPGPCPGPGPAPUP CPAPCPCPCPAPUPGP*U)-3'	rna	13	—	—

Pockets

5 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	356	0.64	0.79	33	empty
2	468	0.62	0.75	50	empty
3	403	0.61	0.77	42	empty
4	94	0.30	0.72	16	empty
5	53	0.27	0.74	10	empty

Interfaces

6 interfaces between chains.

A–B · 3355 Å² buried · 49 hydrogen bonds · protein-protein
A–C · 526 Å² buried · 5 hydrogen bonds · protein-protein
B–R · 415 Å² buried · 11 hydrogen bonds · protein-nucleic
C–S · 358 Å² buried · 10 hydrogen bonds · protein-nucleic
A–R · 324 Å² buried · 11 hydrogen bonds · protein-nucleic

Compared structures

2IZM · MS2-RNA hairpin (C-10) complex · 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 P03612
Elsewhere: RCSB PDB 2IZM · PDBe 2IZM · UniProt P03612

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