MolNFT v1 · #160696 · RNA

58NT RNA L11-binding domain from E. COLI 23S rRNA

6PRV: “58NT RNA L11-binding domain from E. COLI 23S rRNA”. X-ray diffraction, 2 ligands (MG, K), 12 pockets (best druggability 0.75). MolNFT v1 #160696 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6PRV
Type: RNA
Length: 232 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S rRNA
Ligands: MG, K
Pockets: 12 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	23S rRNA	rna	58	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 22 copies · chains A, C, B, D
K · Potassium ion · metal · 3 copies · chains A, B, C

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

Pockets

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	912	0.75	0.80	52	MG
2	498	0.69	0.81	31	empty
3	358	0.67	0.82	23	MG
4	317	0.66	0.82	20	MG
5	120	0.43	0.78	16	empty

Interfaces

2 interfaces between chains.

A–B · 169 Å² buried · 5 hydrogen bonds · nucleic-nucleic
A–C · 129 Å² buried · 2 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

6PRV · 58nt RNA L11-binding domain from E. coli 23S rRNA · the same entry in another collection · chain B against B, 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
Elsewhere: RCSB PDB 6PRV · PDBe 6PRV

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