MolNFT v1 · #141652 · protein + RNA

M. smegmatis P/P state 50S ribosomal subunit

5ZET · 50S ribosomal protein L2: “M. smegmatis P/P state 50S ribosomal subunit”. Electron microscopy, 20 pockets (best druggability 0.88). MolNFT v1 #141652 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZET
Type: protein + RNA
Length: 6,908 residues
Chains: 34
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: A0QSD4, A0QSD1, A0QSD2, A0QSG1, A0QSG4, A0R7F6, A0QS62, A0QS45, A0QSP8, A0QSF9, A0QSG8, A0QSD8, A0QSL9, I7FGD9, A0QV42, A0QYU6, A0R151, A0QSD6, A0QSD3, A0QSG0, I7GFB2, A0R150, I7FJ52, A0QSD9, A0QSG7, A0R215, A0R3I9, A0QS39, A0R7K0, A0QYU7, A0QSL4, A0QTP4
Pockets: 20 · best druggability 0.88

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	50S ribosomal protein L2	protein	273	3% helix, 25% strand	A0QSD4
D	50S ribosomal protein L3	protein	214	9% helix, 35% strand	A0QSD1
E	50S ribosomal protein L4	protein	207	32% helix, 11% strand	A0QSD2
F	50S ribosomal protein L5	protein	181	29% helix, 18% strand	A0QSG1
G	50S ribosomal protein L6	protein	176	19% helix, 36% strand	A0QSG4
H	50S ribosomal protein L9	protein	151	34% helix, 22% strand	A0R7F6
I	50S ribosomal protein L10	protein	126	44% helix, 17% strand	A0QS62
J	50S ribosomal protein L11	protein	133	34% helix, 12% strand	A0QS45
K	50S ribosomal protein L13	protein	147	25% helix, 14% strand	A0QSP8
L	50S ribosomal protein L14	protein	121	5% helix, 35% strand	A0QSF9
M	50S ribosomal protein L15	protein	145	21% helix, 12% strand	A0QSG8
N	50S ribosomal protein L16	protein	134	19% helix, 20% strand	A0QSD8
O	50S ribosomal protein L17	protein	117	46% helix, 12% strand	A0QSL9
P	50S ribosomal protein L18	protein	126	40% helix, 18% strand	I7FGD9
Q	50S ribosomal protein L19	protein	113	16% helix, 42% strand	A0QV42
R	50S ribosomal protein L20	protein	124	73% helix, 0% strand	A0QYU6
S	50S ribosomal protein L21	protein	102	5% helix, 62% strand	A0R151
T	50S ribosomal protein L22	protein	114	28% helix, 35% strand	A0QSD6
U	50S ribosomal protein L23	protein	94	20% helix, 27% strand	A0QSD3
V	50S ribosomal protein L24	protein	97	6% helix, 43% strand	A0QSG0
W	50S ribosomal protein L25	protein	188	14% helix, 42% strand	I7GFB2
X	50S ribosomal protein L27	protein	82	0% helix, 32% strand	A0R150
Y	50S ribosomal protein L28	protein	63	10% helix, 41% strand	I7FJ52
Z	50S ribosomal protein L29	protein	63	71% helix, 0% strand	A0QSD9
B	P-trnafmet	rna	117	—	—
A	23S rRNA	rna	3102	—	—
1	50S ribosomal protein L30	protein	60	30% helix, 18% strand	A0QSG7
2	50S ribosomal protein L31	protein	66	29% helix, 23% strand	A0R215
3	50S ribosomal protein L32	protein	54	24% helix, 19% strand	A0R3I9
4	50S ribosomal protein L33 1	protein	50	6% helix, 44% strand	A0QS39
5	50S ribosomal protein L34	protein	45	51% helix, 0% strand	A0R7K0
6	50S ribosomal protein L35	protein	63	37% helix, 17% strand	A0QYU7
7	50S ribosomal protein L36	protein	37	0% helix, 38% strand	A0QSL4
8	Uncharacterized protein BL37	protein	23	48% 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	934	0.88	0.91	88	empty
2	949	0.88	0.90	89	empty
3	1079	0.86	0.88	98	empty
4	976	0.86	0.88	94	empty
5	790	0.86	0.89	84	empty

Interfaces

66 interfaces between chains.

C–A · 7111 Å² buried · 151 hydrogen bonds · protein-nucleic
D–A · 5086 Å² buried · 111 hydrogen bonds · protein-nucleic
M–A · 4729 Å² buried · 108 hydrogen bonds · protein-nucleic
R–A · 4538 Å² buried · 113 hydrogen bonds · protein-nucleic
E–A · 4383 Å² buried · 90 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 3 disulfide, 1 isopeptide (disulfide, isopeptide).

Compared structures

5ZET · M. smegmatis P/P state 50S ribosomal subunit · the same entry in another collection · chain M against M, 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 I7GFB2
Every structure of UniProt A0R150
Every structure of UniProt I7FJ52
Every structure of UniProt A0QSD9
Every structure of UniProt A0QSG7
Every structure of UniProt A0R215
Every structure of UniProt A0R3I9
Every structure of UniProt A0QS39
Every structure of UniProt A0R7K0
Every structure of UniProt A0QYU7
Every structure of UniProt A0QSL4
Every structure of UniProt A0QTP4
Elsewhere: RCSB PDB 5ZET · PDBe 5ZET · 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 I7GFB2 · UniProt A0R150 · UniProt I7FJ52 · UniProt A0QSD9 · UniProt A0QSG7 · UniProt A0R215 · UniProt A0R3I9 · UniProt A0QS39 · UniProt A0R7K0 · UniProt A0QYU7 · UniProt A0QSL4 · UniProt A0QTP4

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