Research workbench

Cryo-EM structure of mycobacterium smegmatis C(MINUS) 50S ribosomal subunit

Analyse Cryo-EM structure of mycobacterium smegmatis C(MINUS) 50S ribosomal subunit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DZP
Type: protein + RNA
Length: 6,952 residues
Chains: 34
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S rRNA; 5S rRNA; 50S ribosomal protein L2; 50S ribosomal protein L3; 50S ribosomal…
UniProt: A0QSD4, A0QSD1, A0QSD2, A0QSG1, A0QSG4, A0R7F6, A0QS62, A0QS45, A0QSP8, A0QSF9, A0QSG8, A0QSD8, A0QSL9, I7FGD9, A0QV42, A0QYU6, A0R151, A0QSD6, A0QSD3, A0QSG0, A0R3D2, A0R150, A0QSD9, A0QSG7, A0R3I9, A0R551, A0R7K0, A0QYU7, A0QSL4, A0R554, A0QTP4
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 34 distinct chains · 25% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	23S rRNA	rna	3119	—	—
B	5S rRNA	rna	118	—	—
C	50S ribosomal protein L2	protein	275	4% helix, 23% strand	A0QSD4
D	50S ribosomal protein L3	protein	214	9% helix, 35% strand	A0QSD1
E	50S ribosomal protein L4	protein	209	33% helix, 11% strand	A0QSD2
F	50S ribosomal protein L5	protein	182	36% helix, 18% strand	A0QSG1
G	50S ribosomal protein L6	protein	176	19% helix, 39% strand	A0QSG4
H	50S ribosomal protein L9	protein	151	32% helix, 15% strand	A0R7F6
I	50S ribosomal protein L10	protein	126	44% helix, 17% strand	A0QS62
J	50S ribosomal protein L11	protein	133	38% helix, 14% strand	A0QS45
K	50S ribosomal protein L13	protein	146	30% helix, 16% strand	A0QSP8
L	50S ribosomal protein L14	protein	122	7% helix, 32% strand	A0QSF9
M	50S ribosomal protein L15	protein	145	23% helix, 12% strand	A0QSG8
N	50S ribosomal protein L16	protein	136	20% helix, 28% strand	A0QSD8
O	50S ribosomal protein L17	protein	118	53% helix, 14% strand	A0QSL9
P	50S ribosomal protein L18	protein	126	40% helix, 19% strand	I7FGD9
Q	50S ribosomal protein L19	protein	113	9% helix, 42% strand	A0QV42
R	50S ribosomal protein L20	protein	124	70% helix, 0% strand	A0QYU6
S	50S ribosomal protein L21	protein	100	6% helix, 60% strand	A0R151
T	50S ribosomal protein L22	protein	114	34% helix, 39% strand	A0QSD6
U	50S ribosomal protein L23	protein	97	25% helix, 24% strand	A0QSD3
V	50S ribosomal protein L24	protein	97	3% helix, 43% strand	A0QSG0
W	50S ribosomal protein L25	protein	192	11% helix, 39% strand	A0R3D2
X	50S ribosomal protein L27	protein	79	0% helix, 30% strand	A0R150
Z	50S ribosomal protein L29	protein	64	77% helix, 0% strand	A0QSD9
a	50S ribosomal protein L30	protein	59	39% helix, 29% strand	A0QSG7
b	50S ribosomal protein L32	protein	54	24% helix, 22% strand	A0R3I9
c	50S ribosomal protein L33 2	protein	53	0% helix, 11% strand	A0R551
d	50S ribosomal protein L34	protein	46	52% helix, 0% strand	A0R7K0
e	50S ribosomal protein L35	protein	63	30% helix, 11% strand	A0QYU7
f	50S ribosomal protein L36	protein	37	0% helix, 38% strand	A0QSL4
g	50S ribosomal protein L31	protein	64	0% helix, 20% strand	A0R554
y	50S ribosomal protein L28	protein	77	23% helix, 13% strand	—
3	Uncharacterized protein	protein	23	39% helix, 0% strand	A0QTP4

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	1182	0.88	0.90	117	empty
2	954	0.87	0.90	94	empty
3	983	0.87	0.89	97	empty
4	514	0.86	0.93	51	empty
5	1058	0.86	0.88	84	empty

Interfaces

64 interfaces between chains.

A–C · 7100 Å² buried · 128 hydrogen bonds · protein-nucleic
A–D · 4899 Å² buried · 78 hydrogen bonds · protein-nucleic
A–M · 4539 Å² buried · 75 hydrogen bonds · protein-nucleic
A–R · 4359 Å² buried · 98 hydrogen bonds · protein-nucleic
A–E · 4326 Å² buried · 77 hydrogen bonds · protein-nucleic

Compared structures

6DZP · Cryo-EM Structure of Mycobacterium smegmatis C(minus) 50S ribosomal subunit · 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 A0QSD4
Every structure of UniProt A0QSD1
Every structure of UniProt A0QSD2
Every structure of UniProt A0QSG1
Every structure of UniProt A0QSG4
Every structure of UniProt A0R7F6
Every structure of UniProt A0QS62
Every structure of UniProt A0QS45
Every structure of UniProt A0QSP8
Every structure of UniProt A0QSF9
Every structure of UniProt A0QSG8
Every structure of UniProt A0QSD8
Every structure of UniProt A0QSL9
Every structure of UniProt I7FGD9
Every structure of UniProt A0QV42
Every structure of UniProt A0QYU6
Every structure of UniProt A0R151
Every structure of UniProt A0QSD6
Every structure of UniProt A0QSD3
Every structure of UniProt A0QSG0
Every structure of UniProt A0R3D2
Every structure of UniProt A0R150
Every structure of UniProt A0QSD9
Every structure of UniProt A0QSG7
Every structure of UniProt A0R3I9
Every structure of UniProt A0R551
Every structure of UniProt A0R7K0
Every structure of UniProt A0QYU7
Every structure of UniProt A0QSL4
Every structure of UniProt A0R554
Every structure of UniProt A0QTP4
Elsewhere: RCSB PDB 6DZP · PDBe 6DZP · UniProt A0QSD4 · UniProt A0QSD1 · UniProt A0QSD2 · UniProt A0QSG1 · UniProt A0QSG4 · UniProt A0R7F6 · UniProt A0QS62 · UniProt A0QS45 · UniProt A0QSP8 · UniProt A0QSF9 · UniProt A0QSG8 · UniProt A0QSD8 · UniProt A0QSL9 · UniProt I7FGD9 · UniProt A0QV42 · UniProt A0QYU6 · UniProt A0R151 · UniProt A0QSD6 · UniProt A0QSD3 · UniProt A0QSG0 · UniProt A0R3D2 · UniProt A0R150 · UniProt A0QSD9 · UniProt A0QSG7 · UniProt A0R3I9 · UniProt A0R551 · UniProt A0R7K0 · UniProt A0QYU7 · UniProt A0QSL4 · UniProt A0R554 · UniProt A0QTP4

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