Research workbench

50S ribosomal subunit assembly intermediate state 1

Analyse 50S ribosomal subunit assembly intermediate state 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6GC7
Type: protein + RNA
Length: 3,639 residues
Chains: 17
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S ribosomal RNA; 50S ribosomal protein L3; 50S ribosomal protein L4; 50S ribosomal…
UniProt: P60438, P60723, P0AA10, P0ADY3, P02413, P0AG44, P0A7K6, P0A7L3, P0AG48, P61175, P0ADZ0, P60624, P0A7M6, P0A7N4, P0A7P5, P0AG51
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 17 distinct chains · 25% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	23S ribosomal RNA	rna	1901	—	—
D	50S ribosomal protein L3	protein	182	4% helix, 41% strand	P60438
E	50S ribosomal protein L4	protein	201	26% helix, 8% strand	P60723
J	50S ribosomal protein L13	protein	142	35% helix, 18% strand	P0AA10
K	50S ribosomal protein L14	protein	122	2% helix, 34% strand	P0ADY3
L	50S ribosomal protein L15	protein	109	12% helix, 6% strand	P02413
N	50S ribosomal protein L17	protein	120	43% helix, 11% strand	P0AG44
P	50S ribosomal protein L19	protein	114	13% helix, 40% strand	P0A7K6
Q	50S ribosomal protein L20	protein	117	74% helix, 0% strand	P0A7L3
R	50S ribosomal protein L21	protein	103	0% helix, 52% strand	P0AG48
S	50S ribosomal protein L22	protein	110	33% helix, 33% strand	P61175
T	50S ribosomal protein L23	protein	93	26% helix, 31% strand	P0ADZ0
U	50S ribosomal protein L24	protein	102	3% helix, 35% strand	P60624
Y	50S ribosomal protein L29	protein	63	60% helix, 0% strand	P0A7M6
0	50S ribosomal protein L32	protein	56	20% helix, 18% strand	P0A7N4
2	50S ribosomal protein L34	protein	46	50% helix, 0% strand	P0A7P5
Z	50S ribosomal protein L30	protein	58	29% helix, 22% strand	P0AG51

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	1107	0.87	0.89	86	empty
2	782	0.87	0.91	85	empty
3	766	0.87	0.91	78	empty
4	669	0.85	0.90	60	empty
5	545	0.84	0.91	61	empty

Interfaces

31 interfaces between chains.

A–Q · 4227 Å² buried · 80 hydrogen bonds · protein-nucleic
A–E · 4043 Å² buried · 68 hydrogen bonds · protein-nucleic
A–N · 3565 Å² buried · 66 hydrogen bonds · protein-nucleic
A–D · 3159 Å² buried · 57 hydrogen bonds · protein-nucleic
A–J · 2661 Å² buried · 47 hydrogen bonds · protein-nucleic

Compared structures

6GC7 · 50S ribosomal subunit assembly intermediate state 1 · 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
Every structure of UniProt P60438
Every structure of UniProt P60723
Every structure of UniProt P0AA10
Every structure of UniProt P0ADY3
Every structure of UniProt P02413
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
Every structure of UniProt P0AG51
Elsewhere: RCSB PDB 6GC7 · PDBe 6GC7 · UniProt P60438 · UniProt P60723 · UniProt P0AA10 · UniProt P0ADY3 · UniProt P02413 · UniProt P0AG44 · UniProt P0A7K6 · UniProt P0A7L3 · UniProt P0AG48 · UniProt P61175 · UniProt P0ADZ0 · UniProt P60624 · UniProt P0A7M6 · UniProt P0A7N4 · UniProt P0A7P5 · UniProt P0AG51

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