MolNFT v1 · #6545 · RNA

Large ribosomal subunit complexed with R(CC)-da-puromycin

1FFZ · 23S ribosomal RNA: “Large ribosomal subunit complexed with R(CC)-da-puromycin”. X-ray diffraction, 1 ligand (PU), 20 pockets (best druggability 0.78). MolNFT v1 #6545 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1FFZ
Type: RNA
Length: 499 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S ribosomal RNA; R(P*CP*C*)-D(P*A)-R(P*(PU))
Ligands: PU
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	23S ribosomal RNA	rna	496	—	—
B	R(PCPC)-D(PA)-R(P*(PU))	rna	3	—	—

Ligands and binding sites

PU · Puromycin-N-aminophosphonic acid · ligand · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	742	0.78	0.83	53	PU
2	537	0.70	0.81	27	empty
3	890	0.70	0.76	48	empty
4	343	0.69	0.84	33	empty
5	368	0.69	0.83	23	empty

Interfaces

1 interface between chains.

A–B · 505 Å² buried · 21 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

1FFZ · Large ribosomal subunit complexed with R(CC)-da-puromycin · 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
Elsewhere: RCSB PDB 1FFZ · PDBe 1FFZ

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