Research workbench

50S ribosomal subunit without free 5S rRNA and perturbed ptc

Analyse 50S ribosomal subunit without free 5S rRNA and perturbed ptc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WNT
Type: protein + RNA
Length: 6,412 residues
Chains: 31
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 50S ribosomal protein L2; 50S ribosomal protein L3; 50S ribosomal protein L4; 50S…
UniProt: P60422, P60438, P60723, P62399, P0AG55, P0A7R1, P0A7J3, P0A7J7, P0AA10, P0ADY3, P02413, P0AG44, P0C018, P0A7K6, P0A7L3, P0AG48, P61175, P0ADZ0, P60624, P68919, P0A7L8, P0A7M2, P0A7M6, P0AG51, P0A7M9, P0A7N4, P0A7P5, P0A7Q1, P0A7Q6, P0A7L0
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 31 distinct chains · 25% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
b	50S ribosomal protein L2	protein	271	4% helix, 28% strand	P60422
c	50S ribosomal protein L3	protein	209	10% helix, 34% strand	P60438
d	50S ribosomal protein L4	protein	201	33% helix, 12% strand	P60723
e	50S ribosomal protein L5	protein	177	35% helix, 14% strand	P62399
f	50S ribosomal protein L6	protein	176	19% helix, 35% strand	P0AG55
g	50S ribosomal protein L9	protein	53	30% helix, 19% strand	P0A7R1
h	50S ribosomal protein L10	protein	131	27% helix, 3% strand	P0A7J3
i	50S ribosomal protein L11	protein	141	31% helix, 9% strand	P0A7J7
j	50S ribosomal protein L13	protein	142	34% helix, 18% strand	P0AA10
k	50S ribosomal protein L14	protein	122	4% helix, 39% strand	P0ADY3
l	50S ribosomal protein L15	protein	143	18% helix, 13% strand	P02413
n	50S ribosomal protein L17	protein	120	45% helix, 17% strand	P0AG44
o	50S ribosomal protein L18	protein	116	44% helix, 15% strand	P0C018
p	50S ribosomal protein L19	protein	114	16% helix, 41% strand	P0A7K6
q	50S ribosomal protein L20	protein	117	78% helix, 0% strand	P0A7L3
r	50S ribosomal protein L21	protein	103	0% helix, 55% strand	P0AG48
s	50S ribosomal protein L22	protein	110	35% helix, 35% strand	P61175
t	50S ribosomal protein L23	protein	93	26% helix, 33% strand	P0ADZ0
u	50S ribosomal protein L24	protein	102	6% helix, 44% strand	P60624
v	50S ribosomal protein L25	protein	94	18% helix, 47% strand	P68919
w	50S ribosomal protein L27	protein	75	0% helix, 43% strand	P0A7L8
x	50S ribosomal protein L28	protein	77	27% helix, 31% strand	P0A7M2
y	50S ribosomal protein L29	protein	63	65% helix, 0% strand	P0A7M6
z	50S ribosomal protein L30	protein	58	33% helix, 22% strand	P0AG51
A	50S ribosomal protein L31	protein	41	0% helix, 29% strand	P0A7M9
B	50S ribosomal protein L32	protein	56	13% helix, 13% strand	P0A7N4
D	50S ribosomal protein L34	protein	46	59% helix, 0% strand	P0A7P5
E	50S ribosomal protein L35	protein	64	31% helix, 11% strand	P0A7Q1
F	50S ribosomal protein L36	protein	38	16% helix, 26% strand	P0A7Q6
a	50S ribosomal protein L1	protein	134	25% helix, 25% strand	P0A7L0
4	23S-5S joint ribosomal RNA	rna	3025	—	—

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	1027	0.87	0.89	98	empty
2	833	0.87	0.91	81	empty
3	881	0.87	0.90	79	empty
4	1107	0.86	0.88	84	empty
5	582	0.86	0.92	68	empty

Interfaces

52 interfaces between chains.

b–4 · 7296 Å² buried · 177 hydrogen bonds · protein-nucleic
c–4 · 5190 Å² buried · 115 hydrogen bonds · protein-nucleic
l–4 · 4539 Å² buried · 105 hydrogen bonds · protein-nucleic
q–4 · 4276 Å² buried · 106 hydrogen bonds · protein-nucleic
d–4 · 4080 Å² buried · 81 hydrogen bonds · protein-nucleic

Compared structures

6WNT · 50S ribosomal subunit without free 5S rRNA and perturbed PTC · the same entry in another collection · chain l against l, 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 P62399
Every structure of UniProt P0AG55
Every structure of UniProt P0A7R1
Every structure of UniProt P0A7J3
Every structure of UniProt P0A7J7
Every structure of UniProt P0AA10
Every structure of UniProt P0ADY3
Every structure of UniProt P02413
Every structure of UniProt P0AG44
Every structure of UniProt P0C018
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 P68919
Every structure of UniProt P0A7L8
Every structure of UniProt P0A7M2
Every structure of UniProt P0A7M6
Every structure of UniProt P0AG51
Every structure of UniProt P0A7M9
Every structure of UniProt P0A7N4
Every structure of UniProt P0A7P5
Every structure of UniProt P0A7Q1
Every structure of UniProt P0A7Q6
Every structure of UniProt P0A7L0
Elsewhere: RCSB PDB 6WNT · PDBe 6WNT · UniProt P60422 · UniProt P60438 · UniProt P60723 · UniProt P62399 · UniProt P0AG55 · UniProt P0A7R1 · UniProt P0A7J3 · UniProt P0A7J7 · UniProt P0AA10 · UniProt P0ADY3 · UniProt P02413 · UniProt P0AG44 · UniProt P0C018 · UniProt P0A7K6 · UniProt P0A7L3 · UniProt P0AG48 · UniProt P61175 · UniProt P0ADZ0 · UniProt P60624 · UniProt P68919 · UniProt P0A7L8 · UniProt P0A7M2 · UniProt P0A7M6 · UniProt P0AG51 · UniProt P0A7M9 · UniProt P0A7N4 · UniProt P0A7P5 · UniProt P0A7Q1 · UniProt P0A7Q6 · UniProt P0A7L0

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