MolNFT v1 · #29326 · RNA

Crystal structure of a complex of the ribosome large subunit with rapamycin

1Z58 · 23S ribosomal RNA: “Crystal structure of a complex of the ribosome large subunit with rapamycin”. X-ray diffraction, 1 ligand (RAP), 20 pockets (best druggability 0.83). MolNFT v1 #29326 on GenesisL1: 3D structure, binding sites and…

PDB: 1Z58
Type: RNA
Length: 2,766 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S ribosomal RNA
Ligands: RAP
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	23S ribosomal RNA	rna	2766	—	—

Ligands and binding sites

RAP · Rapamycin immunosuppressant drug · ligand · chains 2

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	645	0.83	0.89	62	empty
2	1091	0.82	0.85	89	empty
3	831	0.81	0.85	70	empty
4	1112	0.81	0.83	67	empty
5	813	0.80	0.85	51	empty

Compared structures

1Z58 · Crystal structure of a complex of the ribosome large subunit with rapamycin · the same entry in another collection · chain 2 against 2, 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 1Z58 · PDBe 1Z58

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