MolNFT v1 · #160154 · protein + RNA

E. COLI 50S ribosome bound to compounds 46 and VS1

6PC5 · 23S ribosomal RNA: “E. COLI 50S ribosome bound to compounds 46 and VS1”. Electron microscopy, 1 ligand (O7V), 20 pockets (best druggability 0.88). MolNFT v1 #160154 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6PC5
Type: protein + RNA
Length: 3,986 residues
Chains: 8
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: O7V
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 8 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	271	4% helix, 28% strand	P60422
L	50S ribosomal protein L15	protein	144	20% helix, 9% strand	A0A037Y8L6
M	50S ribosomal protein L4	protein	201	34% helix, 13% strand	D7Z9F6
N	50S ribosomal protein L3	protein	206	9% helix, 38% strand	P60438
O	50S ribosomal protein L13	protein	142	35% helix, 18% strand	D7ZET0
C	Virginiamycin S1	protein	7	0% helix, 0% strand	—

Ligands and binding sites

O7V · (2R)-2-[(3s,4r,5e,10e,12e,14s,16r,26ar)-16-fluoro-14-hydroxy-4,12-dimethyl-1,7,22-trioxo-4,7,8,9,14,15,16, 17,24,25,26,26A-dodecahydro-1H,3H,22H-21,18-(azeno) pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosin-3-yl]propyl isoquinolin-3-ylcarbamate · ligand · chains I, C

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	989	0.88	0.91	105	empty
2	1103	0.88	0.90	99	O7V
3	933	0.87	0.90	85	empty
4	708	0.84	0.89	67	empty
5	533	0.84	0.91	70	empty

Interfaces

9 interfaces between chains.

I–K · 7215 Å² buried · 186 hydrogen bonds · protein-nucleic
I–N · 4898 Å² buried · 113 hydrogen bonds · protein-nucleic
I–L · 4510 Å² buried · 108 hydrogen bonds · protein-nucleic
I–M · 4203 Å² buried · 97 hydrogen bonds · protein-nucleic
I–O · 2748 Å² buried · 60 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 26 modified (nucleotide modification, nonstandard).

Compared structures

6PC5 · E. coli 50S ribosome bound to compounds 46 and VS1 · the same entry in another collection · chain I against I, 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 6PC5 · PDBe 6PC5 · UniProt P60422 · UniProt A0A037Y8L6 · UniProt D7Z9F6 · UniProt P60438 · UniProt D7ZET0

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