Research workbench

E. COLI 50S ribosome licl core particle

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

PDB: 7ODE
Type: protein + RNA
Length: 3,751 residues
Chains: 16
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S rRNA; 50S ribosomal protein L2; 50S ribosomal protein L3; 50S ribosomal protein L4…
UniProt: P60422, P60438, P60723, P0AA10, P0ADY3, P0AG44, P0A7K6, P0A7L3, P0AG48, P61175, P0ADZ0, P60624, P0A7M6, P0A7N4, P0A7P5
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 16 distinct chains · 29% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I	23S rRNA	rna	1990	—	—
K	50S ribosomal protein L2	protein	226	8% helix, 32% strand	P60422
L	50S ribosomal protein L3	protein	183	14% helix, 42% strand	P60438
M	50S ribosomal protein L4	protein	165	45% helix, 16% strand	P60723
R	50S ribosomal protein L13	protein	142	35% helix, 20% strand	P0AA10
S	50S ribosomal protein L14	protein	122	7% helix, 38% strand	P0ADY3
V	50S ribosomal protein L17	protein	120	52% helix, 17% strand	P0AG44
X	50S ribosomal protein L19	protein	114	18% helix, 45% strand	P0A7K6
Y	50S ribosomal protein L20	protein	117	79% helix, 0% strand	P0A7L3
Z	50S ribosomal protein L21	protein	103	0% helix, 57% strand	P0AG48
a	50S ribosomal protein L22	protein	110	40% helix, 35% strand	P61175
b	50S ribosomal protein L23	protein	93	30% helix, 38% strand	P0ADZ0
c	50S ribosomal protein L24	protein	102	3% helix, 45% strand	P60624
g	50S ribosomal protein L29	protein	62	76% helix, 0% strand	P0A7M6
i	50S ribosomal protein L32	protein	56	18% helix, 14% strand	P0A7N4
k	50S ribosomal protein L34	protein	46	57% helix, 0% strand	P0A7P5

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	1154	0.86	0.88	97	empty
2	1155	0.86	0.88	104	empty
3	620	0.85	0.90	67	empty
4	723	0.84	0.89	79	empty
5	793	0.84	0.87	67	empty

Interfaces

29 interfaces between chains.

I–K · 4998 Å² buried · 124 hydrogen bonds · protein-nucleic
I–Y · 4061 Å² buried · 103 hydrogen bonds · protein-nucleic
I–V · 3565 Å² buried · 83 hydrogen bonds · protein-nucleic
I–L · 3265 Å² buried · 57 hydrogen bonds · protein-nucleic
I–R · 2675 Å² buried · 60 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

7ODE · E. coli 50S ribosome LiCl core particle · 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 P60438
Every structure of UniProt P60723
Every structure of UniProt P0AA10
Every structure of UniProt P0ADY3
Every structure of UniProt P0AG44
Every structure of UniProt P0A7K6
Every structure of UniProt P0A7L3
Every structure of UniProt P0AG48
Every structure of UniProt P61175
Every structure of UniProt P0ADZ0
Every structure of UniProt P60624
Every structure of UniProt P0A7M6
Every structure of UniProt P0A7N4
Every structure of UniProt P0A7P5
Elsewhere: RCSB PDB 7ODE · PDBe 7ODE · UniProt P60422 · UniProt P60438 · UniProt P60723 · UniProt P0AA10 · UniProt P0ADY3 · UniProt P0AG44 · UniProt P0A7K6 · UniProt P0A7L3 · UniProt P0AG48 · UniProt P61175 · UniProt P0ADZ0 · UniProt P60624 · UniProt P0A7M6 · UniProt P0A7N4 · UniProt P0A7P5

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