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Molecular basis of box C/D RNA-protein interaction: co-crystal structure of the archaeal srnp intiation complex

Analyse Molecular basis of box C/D RNA-protein interaction: co-crystal structure of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1RLG
Type: protein + RNA
Length: 280 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 25-mer; 50S ribosomal protein L7AE
UniProt: O29494
Pockets: 1 · best druggability 0.26

Structure

x-ray diffraction · 3 distinct chains · 46% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	25-mer	rna	25	—	—
A	50S ribosomal protein L7AE	protein	113	49% helix, 17% strand	O29494
B	50S ribosomal protein L7AE	protein	117	44% helix, 16% strand	O29494

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	53	0.26	0.74	13	empty

Interfaces

3 interfaces between chains.

C–A · 661 Å² buried · 27 hydrogen bonds · protein-nucleic
D–B · 635 Å² buried · 29 hydrogen bonds · protein-nucleic
C–D · 189 Å² buried · 11 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 6 modified (nucleotide modification).

Compared structures

1RLG · Molecular basis of Box C/D RNA-protein interaction: co-crystal structure of the Archaeal… · the same entry in another collection · chain C against C, TM-score 1.00
O29494 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L7AE (O29494) · a predicted model of the same protein · chain B 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 O29494
Elsewhere: RCSB PDB 1RLG · PDBe 1RLG · UniProt O29494

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