MolNFT v1 · #140036 · protein + RNA

Small subunit of toxoplasma gondii ribosome

5XXU · 18S RNA: “Small subunit of toxoplasma gondii ribosome”. Electron microscopy, 20 pockets (best druggability 0.88). MolNFT v1 #140036 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XXU
Type: protein + RNA
Length: 6,000 residues
Chains: 34
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 18S RNA; Ribosomal protein US2; Ribosomal protein ES1; Ribosomal protein US5; Ribosomal…
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 34 distinct chains · 32% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	18S RNA	rna	1619	—	—
A	Ribosomal protein US2	protein	198	33% helix, 11% strand	—
B	Ribosomal protein ES1	protein	212	31% helix, 27% strand	—
C	Ribosomal protein US5	protein	225	32% helix, 25% strand	—
D	Ribosomal protein US3	protein	200	39% helix, 26% strand	—
E	Ribosomal protein ES4	protein	259	13% helix, 32% strand	—
F	Ribosomal protein US7	protein	187	44% helix, 5% strand	—
G	Ribosomal protein ES6	protein	220	24% helix, 19% strand	—
H	Ribosomal protein ES7	protein	177	40% helix, 19% strand	—
I	Ribosomal protein ES8	protein	185	27% helix, 25% strand	—
J	Ribosomal protein US4	protein	178	48% helix, 3% strand	—
K	Ribosomal protein ES10	protein	94	39% helix, 10% strand	—
L	Ribosomal protein US17	protein	147	3% helix, 28% strand	—
M	Ribosomal protein ES12	protein	99	44% helix, 8% strand	—
N	Ribosomal protein US15	protein	150	55% helix, 0% strand	—
O	Ribosomal protein US11	protein	129	27% helix, 22% strand	—
P	Ribosomal protein US19	protein	115	23% helix, 11% strand	—
Q	Ribosomal protein US9	protein	138	36% helix, 18% strand	—
R	Ribosomal protein ES17	protein	117	56% helix, 3% strand	—
S	Ribosomal protein US13	protein	135	39% helix, 4% strand	—
T	Ribosomal protein ES19	protein	151	48% helix, 9% strand	—
U	Ribosomal protein US10	protein	103	25% helix, 31% strand	—
V	Ribosomal protein ES21	protein	80	18% helix, 18% strand	—
W	Ribosomal protein US8	protein	129	32% helix, 29% strand	—
X	Ribosomal protein US12	protein	135	26% helix, 26% strand	—
Y	Ribosomal protein ES24	protein	128	34% helix, 28% strand	—
Z	Ribosomal protein ES25	protein	71	44% helix, 11% strand	—
a	Ribosomal protein ES26	protein	99	15% helix, 18% strand	—
b	Ribosomal protein ES27	protein	79	8% helix, 23% strand	—
c	Ribosomal protein ES28	protein	57	0% helix, 47% strand	—
d	Ribosomal protein US14	protein	51	20% helix, 8% strand	—
e	Ribosomal protein ES30	protein	50	32% helix, 2% strand	—
f	Ribosomal protein ES31	protein	45	0% helix, 18% strand	—
m	Ribosomal protein EL41	protein	38	63% helix, 0% strand	—

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	792	0.88	0.93	95	empty
2	834	0.88	0.92	88	empty
3	768	0.87	0.91	108	empty
4	495	0.85	0.93	59	empty
5	609	0.85	0.91	74	empty

Interfaces

88 interfaces between chains.

2–G · 4896 Å² buried · 96 hydrogen bonds · protein-nucleic
2–E · 4556 Å² buried · 73 hydrogen bonds · protein-nucleic
2–I · 3800 Å² buried · 88 hydrogen bonds · protein-nucleic
2–J · 3741 Å² buried · 77 hydrogen bonds · protein-nucleic
2–X · 3508 Å² buried · 66 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5XXU · Small subunit of Toxoplasma gondii ribosome · the same entry in another collection · chain A against A, 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
Elsewhere: RCSB PDB 5XXU · PDBe 5XXU

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