MolNFT v1 · #177966 · protein + RNA

Cryo-EM structure of mycobacterium tuberculosis 50S ribosome subunit bound with clarithromycin

7F0D · 50S ribosomal protein L32: “Cryo-EM structure of mycobacterium tuberculosis 50S ribosome subunit bound with clarithromycin”. Electron microscopy, 2 ligands (CTY, MG), 20 pockets (best druggability 0.88). MolNFT v1 #177966 on…

PDB: 7F0D
Type: protein + RNA
Length: 6,449 residues
Chains: 31
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 50S ribosomal protein L32; 50S ribosomal protein L33; 50S ribosomal protein L34; 50S…
UniProt: A0A045IMI5, A0A045HU86, A0A3E0V610, A0A045KKY9, A0A3E0V5U0, A0A045HLX7, A0A045H5T7, A0A045HU18, A0A045J9H1, A0A045HUU0, A0A045JJU1, A0A045JW48, A0A0T9D5H2, A0A045HTP7, A0A654TTE7, A0A045IWV9, A0A045IVA2, A0A045JK28, A0A045IDD2, A0A045KJ85, P9WHC3, A0A045H760, A0A045J9M3, A0A045IXU4, A0A045JAK4, A0A045K0G1, A0A045IDB8, A0A045IQ64, A0A045H4J2
Ligands: CTY, MG
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 31 distinct chains · 20% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	50S ribosomal protein L32	protein	53	26% helix, 4% strand	A0A045IMI5
1	50S ribosomal protein L33	protein	48	0% helix, 23% strand	A0A045HU86
2	50S ribosomal protein L34	protein	42	55% helix, 0% strand	A0A3E0V610
3	50S ribosomal protein L35	protein	62	29% helix, 13% strand	A0A045KKY9
4	50S ribosomal protein L36	protein	37	0% helix, 24% strand	A0A3E0V5U0
6	50S ribosomal protein L31	protein	45	0% helix, 4% strand	A0A045HLX7
A	23S rRNA	rna	3118	—	—
B	5S ribosomal RNA	rna	115	—	—
C	50S ribosomal protein L2	protein	272	5% helix, 19% strand	A0A045H5T7
D	50S ribosomal protein L3	protein	213	8% helix, 31% strand	A0A045HU18
E	50S ribosomal protein L4	protein	207	31% helix, 8% strand	A0A045J9H1
F	50S ribosomal protein L5	protein	170	26% helix, 11% strand	A0A045HUU0
G	50S ribosomal protein L6	protein	174	17% helix, 19% strand	A0A045JJU1
H	50S ribosomal protein L9	protein	47	11% helix, 4% strand	A0A045JW48
J	50S ribosomal protein L13	protein	146	30% helix, 14% strand	A0A0T9D5H2
K	50S ribosomal protein L14	protein	121	0% helix, 26% strand	A0A045HTP7
L	50S ribosomal protein L15	protein	142	15% helix, 5% strand	A0A654TTE7
M	50S ribosomal protein L16	protein	134	20% helix, 22% strand	A0A045IWV9
N	50S ribosomal protein L17	protein	116	51% helix, 16% strand	A0A045IVA2
O	50S ribosomal protein L18	protein	116	34% helix, 16% strand	A0A045JK28
P	50S ribosomal protein L19	protein	112	9% helix, 37% strand	A0A045IDD2
Q	50S ribosomal protein L20	protein	122	70% helix, 0% strand	A0A045KJ85
R	50S ribosomal protein L21	protein	98	4% helix, 46% strand	P9WHC3
S	50S ribosomal protein L22	protein	113	34% helix, 31% strand	A0A045H760
T	50S ribosomal protein L23	protein	98	21% helix, 26% strand	A0A045J9M3
U	50S ribosomal protein L24	protein	90	3% helix, 32% strand	A0A045IXU4
V	50S ribosomal protein L25	protein	177	5% helix, 29% strand	A0A045JAK4
W	50S ribosomal protein L27	protein	74	0% helix, 9% strand	A0A045K0G1
X	50S ribosomal protein L28	protein	63	0% helix, 19% strand	A0A045IDB8
Y	50S ribosomal protein L29	protein	65	71% helix, 0% strand	A0A045IQ64
Z	50S ribosomal protein L30	protein	59	29% helix, 20% strand	A0A045H4J2

Ligands and binding sites

CTY · Clarithromycin · ligand · chains A, S
MG · Magnesium ion · metal · chains A, E

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	997	0.88	0.90	81	empty
2	1152	0.88	0.90	112	empty
3	719	0.87	0.92	83	empty
4	1104	0.87	0.89	102	empty
5	751	0.86	0.90	84	empty

Interfaces

56 interfaces between chains.

A–C · 7619 Å² buried · 160 hydrogen bonds · protein-nucleic
A–D · 4941 Å² buried · 108 hydrogen bonds · protein-nucleic
A–L · 4675 Å² buried · 111 hydrogen bonds · protein-nucleic
A–E · 4527 Å² buried · 102 hydrogen bonds · protein-nucleic
A–Q · 4381 Å² buried · 113 hydrogen bonds · protein-nucleic

Compared structures

7F0D · Cryo-EM structure of Mycobacterium tuberculosis 50S ribosome subunit bound with… · the same entry in another collection · chain 0 against 0, 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 A0A045IMI5
Every structure of UniProt A0A045HU86
Every structure of UniProt A0A3E0V610
Every structure of UniProt A0A045KKY9
Every structure of UniProt A0A3E0V5U0
Every structure of UniProt A0A045HLX7
Every structure of UniProt A0A045H5T7
Every structure of UniProt A0A045HU18
Every structure of UniProt A0A045J9H1
Every structure of UniProt A0A045HUU0
Every structure of UniProt A0A045JJU1
Every structure of UniProt A0A045JW48
Every structure of UniProt A0A0T9D5H2
Every structure of UniProt A0A045HTP7
Every structure of UniProt A0A654TTE7
Every structure of UniProt A0A045IWV9
Every structure of UniProt A0A045IVA2
Every structure of UniProt A0A045JK28
Every structure of UniProt A0A045IDD2
Every structure of UniProt A0A045KJ85
Every structure of UniProt P9WHC3
Every structure of UniProt A0A045H760
Every structure of UniProt A0A045J9M3
Every structure of UniProt A0A045IXU4
Every structure of UniProt A0A045JAK4
Every structure of UniProt A0A045K0G1
Every structure of UniProt A0A045IDB8
Every structure of UniProt A0A045IQ64
Every structure of UniProt A0A045H4J2
Elsewhere: RCSB PDB 7F0D · PDBe 7F0D · UniProt A0A045IMI5 · UniProt A0A045HU86 · UniProt A0A3E0V610 · UniProt A0A045KKY9 · UniProt A0A3E0V5U0 · UniProt A0A045HLX7 · UniProt A0A045H5T7 · UniProt A0A045HU18 · UniProt A0A045J9H1 · UniProt A0A045HUU0 · UniProt A0A045JJU1 · UniProt A0A045JW48 · UniProt A0A0T9D5H2 · UniProt A0A045HTP7 · UniProt A0A654TTE7 · UniProt A0A045IWV9 · UniProt A0A045IVA2 · UniProt A0A045JK28 · UniProt A0A045IDD2 · UniProt A0A045KJ85 · UniProt P9WHC3 · UniProt A0A045H760 · UniProt A0A045J9M3 · UniProt A0A045IXU4 · UniProt A0A045JAK4 · UniProt A0A045K0G1 · UniProt A0A045IDB8 · UniProt A0A045IQ64 · UniProt A0A045H4J2

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