Research workbench

E. COLI 50S ribosome bound to compound 47

Analyse E. COLI 50S ribosome bound to compound 47 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PC6
Type: protein + RNA
Length: 3,978 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S ribosomal RNA; 5S ribosomal RNA; 50S ribosomal protein L2; 50S ribosomal protein L15…
UniProt: P60422, A0A037Y8L6, D7Z9F6, P60438, D7ZET0
Ligands: O7S
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 7 distinct chains · 18% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I	23S ribosomal RNA	rna	2897	—	—
J	5S ribosomal RNA	rna	118	—	—
K	50S ribosomal protein L2	protein	270	4% helix, 27% strand	P60422
L	50S ribosomal protein L15	protein	144	17% helix, 10% strand	A0A037Y8L6
M	50S ribosomal protein L4	protein	201	34% helix, 12% strand	D7Z9F6
N	50S ribosomal protein L3	protein	206	9% helix, 35% strand	P60438
O	50S ribosomal protein L13	protein	142	33% helix, 18% strand	D7ZET0

Ligands and binding sites

O7S · (3r,4r,5e,10e,12e,14s,16r,26ar)-16-fluoro-14-hydroxy-12-methyl-3-(propan-2-yl)-4-(prop-2-en-1-yl)-3,4,8,9, 14,15,16,17,24,25,26,26A-dodecahydro-1H,7H,22H-21,18-(azeno)pyrrolo[2,1-C][1,8,4, 19]dioxadiazacyclotetracosine-1,7,22-trione · ligand · chains I

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	902	0.87	0.90	85	empty
2	563	0.84	0.90	72	empty
3	919	0.84	0.87	68	empty
4	625	0.83	0.89	71	empty
5	454	0.83	0.91	49	empty

Interfaces

8 interfaces between chains.

I–K · 7121 Å² buried · 189 hydrogen bonds · protein-nucleic
I–N · 4900 Å² buried · 107 hydrogen bonds · protein-nucleic
I–L · 4523 Å² buried · 95 hydrogen bonds · protein-nucleic
I–M · 4172 Å² buried · 92 hydrogen bonds · protein-nucleic
I–O · 2724 Å² buried · 60 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 21 modified (nucleotide modification).

Compared structures

6PC6 · E. coli 50S ribosome bound to compound 47 · the same entry in another collection · chain K against K, 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
Every structure of UniProt P60422
Every structure of UniProt A0A037Y8L6
Every structure of UniProt D7Z9F6
Every structure of UniProt P60438
Every structure of UniProt D7ZET0
Elsewhere: RCSB PDB 6PC6 · PDBe 6PC6 · UniProt P60422 · UniProt A0A037Y8L6 · UniProt D7Z9F6 · UniProt P60438 · UniProt D7ZET0

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