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Crystal structure of a conserved ribosomal protein-RNA complex

Analyse Crystal structure of a conserved ribosomal protein-RNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1QA6
Type: protein + RNA
Length: 250 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 58 nucleotide ribosomal RNA domain; Ribosomal protein L11
UniProt: P56210
Ligands: MG, OS
Pockets: 7 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 58% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	58 nucleotide ribosomal RNA domain	rna	58	—	—
A, B	Ribosomal protein L11	protein	67	58% helix, 0% strand	P56210

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains C, D
OS · Osmium ion · metal · 4 copies · chains C, D

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

Pockets

7 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	900	0.69	0.76	58	OS
2	315	0.66	0.83	22	MG
3	298	0.66	0.83	21	MG, OS
4	90	0.33	0.75	15	empty
5	52	0.27	0.75	11	empty

Interfaces

4 interfaces between chains.

C–A · 977 Å² buried · 26 hydrogen bonds · protein-nucleic
D–B · 975 Å² buried · 26 hydrogen bonds · protein-nucleic
C–D · 84 Å² buried · 3 hydrogen bonds · nucleic-nucleic
D–A · 72 Å² buried · 0 hydrogen bonds · protein-nucleic

Compared structures

1QA6 · Crystal structure of a conserved ribosomal protein-RNA complex · the same entry in another collection · chain C against C, TM-score 1.00
P56210 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L11 (P56210) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P56210
Elsewhere: RCSB PDB 1QA6 · PDBe 1QA6 · UniProt P56210

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