Research workbench

Mycoplasma pneumoniae 50S subunit of ribosomes in chloramphenicol- treated cells

Analyse Mycoplasma pneumoniae 50S subunit of ribosomes in chloramphenicol- treated cells in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7OOD
Type: protein + RNA
Length: 6,433 residues
Chains: 31
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S ribosomal RNA; 5S ribosomal RNA; 50S ribosomal protein L29; 50S ribosomal protein L2…
UniProt: Q50310, P75577, P75579, Q50303, Q50300, P75178, Q59547, P78026, P75458, P75238, P78006, P52864, P75447, P75133, P75578, P75171, P78020, P78015, Q50306, P75580, P41204, P78023, Q50308, Q50302, Q50307, P75575, P75540, P75550, P75240
Ligands: CLM, MG, ZN, K
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 31 distinct chains · 24% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
3	23S ribosomal RNA	rna	2879	—	—
4	5S ribosomal RNA	rna	105	—	—
w	50S ribosomal protein L29	protein	99	71% helix, 0% strand	Q50310
a	50S ribosomal protein L2	protein	285	7% helix, 21% strand	P75577
c	50S ribosomal protein L4	protein	210	28% helix, 9% strand	P75579
e	50S ribosomal protein L6	protein	176	20% helix, 35% strand	Q50303
k	50S ribosomal protein L15	protein	148	16% helix, 13% strand	Q50300
i	50S ribosomal protein L13	protein	144	31% helix, 15% strand	P75178
m	50S ribosomal protein L17	protein	119	49% helix, 15% strand	Q59547
q	50S ribosomal protein L21	protein	99	0% helix, 52% strand	P78026
u	50S ribosomal protein L27	protein	86	0% helix, 40% strand	P75458
y	50S ribosomal protein L32	protein	56	20% helix, 18% strand	P75238
0	50S ribosomal protein L34	protein	47	53% helix, 0% strand	P78006
2	50S ribosomal protein L36	protein	37	8% helix, 38% strand	P52864
1	50S ribosomal protein L35	protein	59	34% helix, 10% strand	P75447
o	50S ribosomal protein L19	protein	115	10% helix, 37% strand	P75133
s	50S ribosomal protein L23	protein	92	20% helix, 24% strand	P75578
v	50S ribosomal protein L28	protein	63	19% helix, 33% strand	P75171
x	50S ribosomal protein L31	protein	44	0% helix, 27% strand	P78020
z	50S ribosomal protein L33 1	protein	50	0% helix, 48% strand	P78015
d	50S ribosomal protein L5	protein	175	33% helix, 19% strand	Q50306
b	50S ribosomal protein L3	protein	229	9% helix, 37% strand	P75580
l	50S ribosomal protein L16	protein	136	20% helix, 21% strand	P41204
p	50S ribosomal protein L20	protein	114	68% helix, 0% strand	P78023
j	50S ribosomal protein L14	protein	122	7% helix, 39% strand	Q50308
n	50S ribosomal protein L18	protein	112	34% helix, 22% strand	Q50302
t	50S ribosomal protein L24	protein	96	0% helix, 25% strand	Q50307
r	50S ribosomal protein L22	protein	139	44% helix, 24% strand	P75575
f	50S ribosomal protein L9	protein	144	28% helix, 24% strand	P75540
h	50S ribosomal protein L11	protein	128	38% helix, 10% strand	P75550
g	50S ribosomal protein L10	protein	125	45% helix, 20% strand	P75240

Ligands and binding sites

CLM · Chloramphenicol · ligand · chains 3
MG · Magnesium ion · metal · 25 copies · chains 3, k, a, y
ZN · Zinc ion · metal · 3 copies · chains y, 2, z
K · Potassium ion · metal · chains 3

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	1135	0.88	0.90	97	empty
2	845	0.87	0.91	83	MG
3	655	0.87	0.92	77	MG
4	708	0.85	0.90	74	empty
5	627	0.85	0.91	78	MG

Interfaces

56 interfaces between chains.

3–a · 7480 Å² buried · 150 hydrogen bonds · protein-nucleic
3–b · 5208 Å² buried · 99 hydrogen bonds · protein-nucleic
3–k · 4866 Å² buried · 103 hydrogen bonds · protein-nucleic
3–c · 4417 Å² buried · 81 hydrogen bonds · protein-nucleic
3–p · 3903 Å² buried · 83 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7OOD · Mycoplasma pneumoniae 50S subunit of ribosomes in chloramphenicol-treated cells · the same entry in another collection · chain u against u, 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 Q50310
Every structure of UniProt P75577
Every structure of UniProt P75579
Every structure of UniProt Q50303
Every structure of UniProt Q50300
Every structure of UniProt P75178
Every structure of UniProt Q59547
Every structure of UniProt P78026
Every structure of UniProt P75458
Every structure of UniProt P75238
Every structure of UniProt P78006
Every structure of UniProt P52864
Every structure of UniProt P75447
Every structure of UniProt P75133
Every structure of UniProt P75578
Every structure of UniProt P75171
Every structure of UniProt P78020
Every structure of UniProt P78015
Every structure of UniProt Q50306
Every structure of UniProt P75580
Every structure of UniProt P41204
Every structure of UniProt P78023
Every structure of UniProt Q50308
Every structure of UniProt Q50302
Every structure of UniProt Q50307
Every structure of UniProt P75575
Every structure of UniProt P75540
Every structure of UniProt P75550
Every structure of UniProt P75240
Elsewhere: RCSB PDB 7OOD · PDBe 7OOD · UniProt Q50310 · UniProt P75577 · UniProt P75579 · UniProt Q50303 · UniProt Q50300 · UniProt P75178 · UniProt Q59547 · UniProt P78026 · UniProt P75458 · UniProt P75238 · UniProt P78006 · UniProt P52864 · UniProt P75447 · UniProt P75133 · UniProt P75578 · UniProt P75171 · UniProt P78020 · UniProt P78015 · UniProt Q50306 · UniProt P75580 · UniProt P41204 · UniProt P78023 · UniProt Q50308 · UniProt Q50302 · UniProt Q50307 · UniProt P75575 · UniProt P75540 · UniProt P75550 · UniProt P75240

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