MolNFT v1 · #141653 · protein + RNA

M. smegmatis P/P state 30S ribosomal subunit

5ZEU · 16S rRNA: “M. smegmatis P/P state 30S ribosomal subunit”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #141653 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZEU
Type: protein + RNA
Length: 3,989 residues
Chains: 22
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 16S rRNA; 30S ribosomal protein S3; 30S ribosomal protein S5; 30S ribosomal protein S7…
UniProt: A0QSD7, A0QSG6, A0QS97, A0QSG3, A0QSP9, A0QSD0, A0QSL6, A0QS96, A0QVQ3, A0QSE0, A0R7F7, A0QSD5, A0R102, A0QSG2, A0QVB8, A0QSL7, A0A0D6J3X3, A0QSL5, A0QV37, A0QR10
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 22 distinct chains · 37% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
a	16S rRNA	rna	1506	—	—
c	30S ribosomal protein S3	protein	210	27% helix, 23% strand	A0QSD7
e	30S ribosomal protein S5	protein	198	32% helix, 30% strand	A0QSG6
g	30S ribosomal protein S7	protein	156	58% helix, 5% strand	A0QS97
h	30S ribosomal protein S8	protein	130	27% helix, 25% strand	A0QSG3
i	30S ribosomal protein S9	protein	126	33% helix, 18% strand	A0QSP9
j	30S ribosomal protein S10	protein	97	28% helix, 41% strand	A0QSD0
k	30S ribosomal protein S11	protein	117	29% helix, 25% strand	A0QSL6
l	30S ribosomal protein S12	protein	122	4% helix, 25% strand	A0QS96
o	30S ribosomal protein S15	protein	87	72% helix, 0% strand	A0QVQ3
q	30S ribosomal protein S17	protein	92	0% helix, 35% strand	A0QSE0
r	30S ribosomal protein S18 2	protein	64	39% helix, 3% strand	A0R7F7
s	30S ribosomal protein S19	protein	78	28% helix, 17% strand	A0QSD5
t	30S ribosomal protein S20	protein	84	82% helix, 0% strand	A0R102
v	P-trnafmet	rna	77	—	—
n	30S ribosomal protein S14 type Z	protein	60	30% helix, 8% strand	A0QSG2
b	30S ribosomal protein S2	protein	228	46% helix, 12% strand	A0QVB8
d	30S ribosomal protein S4	protein	200	44% helix, 7% strand	A0QSL7
f	30S ribosomal protein S6	protein	96	30% helix, 33% strand	A0A0D6J3X3
m	30S ribosomal protein S13	protein	116	49% helix, 0% strand	A0QSL5
p	30S ribosomal protein S16	protein	113	33% helix, 23% strand	A0QV37
u	Conserved domain protein	protein	32	88% helix, 0% strand	A0QR10

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	990	0.85	0.88	84	empty
2	675	0.85	0.90	73	empty
3	1091	0.85	0.87	87	empty
4	1063	0.85	0.86	95	empty
5	924	0.83	0.86	51	empty

Interfaces

42 interfaces between chains.

a–l · 3061 Å² buried · 68 hydrogen bonds · protein-nucleic
a–i · 3052 Å² buried · 96 hydrogen bonds · protein-nucleic
a–d · 3005 Å² buried · 73 hydrogen bonds · protein-nucleic
a–q · 2706 Å² buried · 52 hydrogen bonds · protein-nucleic
a–t · 2446 Å² buried · 56 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5ZEU · M. smegmatis P/P state 30S ribosomal subunit · the same entry in another collection · chain o against o, 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 A0QSD7
Every structure of UniProt A0QSG6
Every structure of UniProt A0QS97
Every structure of UniProt A0QSG3
Every structure of UniProt A0QSP9
Every structure of UniProt A0QSD0
Every structure of UniProt A0QSL6
Every structure of UniProt A0QS96
Every structure of UniProt A0QVQ3
Every structure of UniProt A0QSE0
Every structure of UniProt A0R7F7
Every structure of UniProt A0QSD5
Every structure of UniProt A0R102
Every structure of UniProt A0QSG2
Every structure of UniProt A0QVB8
Every structure of UniProt A0QSL7
Every structure of UniProt A0A0D6J3X3
Every structure of UniProt A0QSL5
Every structure of UniProt A0QV37
Every structure of UniProt A0QR10
Elsewhere: RCSB PDB 5ZEU · PDBe 5ZEU · UniProt A0QSD7 · UniProt A0QSG6 · UniProt A0QS97 · UniProt A0QSG3 · UniProt A0QSP9 · UniProt A0QSD0 · UniProt A0QSL6 · UniProt A0QS96 · UniProt A0QVQ3 · UniProt A0QSE0 · UniProt A0R7F7 · UniProt A0QSD5 · UniProt A0R102 · UniProt A0QSG2 · UniProt A0QVB8 · UniProt A0QSL7 · UniProt A0A0D6J3X3 · UniProt A0QSL5 · UniProt A0QV37 · UniProt A0QR10

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.