MolNFT v1 · #185859 · protein + RNA

Specific features and methylation sites of a plant ribosome. 40S body ribosomal subunit.

7QIX · 18S rRNA body: “Specific features and methylation sites of a plant ribosome. 40S body ribosomal subunit.”. Electron microscopy, 3 ligands (MG, K, ZN), 20 pockets (best druggability 0.88). MolNFT v1 #185859 on GenesisL1: 3D…

PDB: 7QIX
Type: protein + RNA
Length: 4,022 residues
Chains: 22
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 18S rRNA body; 60S ribosomal protein L41; 40S ribosomal protein sa; 40S ribosomal protein…
UniProt: K4C3A4, A0A3Q7H1U4, A0A3Q7I881, A0A3Q7H0E8, A0A3Q7HJ03, K4C998, P49215, A0A3Q7G7P4, K4D3L7, A0A3Q7GRY8, A0A3Q7G7F0, A0A3Q7HSH1, K4ATQ2, K4CYU9, Q38JI8, A0A3Q7I5D6, A0A1U8DQX3, A0A0V0GRY5, A0A1U7YEG5, A0A3Q7GQ29
Ligands: MG, K, ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 22 distinct chains · 32% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	18S rRNA body	rna	1110	—	—
D	60S ribosomal protein L41	protein	25	80% helix, 0% strand	K4C3A4
E	40S ribosomal protein sa	protein	202	37% helix, 15% strand	A0A3Q7H1U4
F	40S ribosomal protein S3A	protein	215	32% helix, 36% strand	A0A3Q7I881
G	40S body ribosomal protein ES4	protein	261	20% helix, 33% strand	—
H	40S ribosomal protein S7	protein	187	43% helix, 22% strand	A0A3Q7H0E8
I	40S ribosomal protein S8	protein	184	27% helix, 28% strand	A0A3Q7HJ03
J	RIBOSOMAL_S17_N domain-containing protein	protein	147	3% helix, 31% strand	K4C998
K	40S ribosomal protein S17	protein	44	20% helix, 14% strand	P49215
L	40S ribosomal protein S21	protein	82	24% helix, 27% strand	A0A3Q7G7P4
M	40S body ribosomal protein US12	protein	141	24% helix, 29% strand	K4D3L7
N	40S ribosomal protein S26	protein	98	15% helix, 23% strand	A0A3Q7GRY8
O	S5 drbm domain-containing protein	protein	220	33% helix, 26% strand	A0A3Q7G7F0
P	40S ribosomal protein S6	protein	237	27% helix, 25% strand	A0A3Q7HSH1
Q	40S body ribosomal protein US4	protein	184	54% helix, 5% strand	K4ATQ2
R	30S ribosomal protein S15, chloroplastic	protein	150	57% helix, 0% strand	K4CYU9
S	Ribosomal protein S14	protein	132	24% helix, 26% strand	Q38JI8
U	40S ribosomal protein S24	protein	126	33% helix, 29% strand	A0A3Q7I5D6
V	40S ribosomal protein S27	protein	68	13% helix, 16% strand	A0A1U8DQX3
W	40S ribosomal protein S30	protein	48	38% helix, 0% strand	A0A0V0GRY5
T	40S ribosomal protein S15A-1	protein	129	34% helix, 27% strand	A0A1U7YEG5
X	Ribosomal protein L19	protein	32	91% helix, 0% strand	A0A3Q7GQ29

Ligands and binding sites

MG · Magnesium ion · metal · 60 copies · chains 2, N, R, S, F, M, P
K · Potassium ion · metal · 19 copies · chains 2, G, N, R, J, M
ZN · Zinc ion · metal · chains N

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	1106	0.88	0.90	88	MG
2	1125	0.87	0.89	117	K, MG
3	1101	0.87	0.89	89	MG
4	781	0.86	0.89	80	MG
5	576	0.85	0.92	61	K, MG

Interfaces

55 interfaces between chains.

2–P · 5234 Å² buried · 121 hydrogen bonds · protein-nucleic
2–G · 4127 Å² buried · 70 hydrogen bonds · protein-nucleic
2–I · 3983 Å² buried · 109 hydrogen bonds · protein-nucleic
2–Q · 3896 Å² buried · 89 hydrogen bonds · protein-nucleic
2–M · 3491 Å² buried · 87 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 51 modified (nucleotide modification, nonstandard).

Compared structures

7QIX · Specific features and methylation sites of a plant ribosome. 40S body ribosomal subunit. · the same entry in another collection · chain X against X, 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 K4C3A4
Every structure of UniProt A0A3Q7H1U4
Every structure of UniProt A0A3Q7I881
Every structure of UniProt A0A3Q7H0E8
Every structure of UniProt A0A3Q7HJ03
Every structure of UniProt K4C998
Every structure of UniProt P49215
Every structure of UniProt A0A3Q7G7P4
Every structure of UniProt K4D3L7
Every structure of UniProt A0A3Q7GRY8
Every structure of UniProt A0A3Q7G7F0
Every structure of UniProt A0A3Q7HSH1
Every structure of UniProt K4ATQ2
Every structure of UniProt K4CYU9
Every structure of UniProt Q38JI8
Every structure of UniProt A0A3Q7I5D6
Every structure of UniProt A0A1U8DQX3
Every structure of UniProt A0A0V0GRY5
Every structure of UniProt A0A1U7YEG5
Every structure of UniProt A0A3Q7GQ29
Elsewhere: RCSB PDB 7QIX · PDBe 7QIX · UniProt K4C3A4 · UniProt A0A3Q7H1U4 · UniProt A0A3Q7I881 · UniProt A0A3Q7H0E8 · UniProt A0A3Q7HJ03 · UniProt K4C998 · UniProt P49215 · UniProt A0A3Q7G7P4 · UniProt K4D3L7 · UniProt A0A3Q7GRY8 · UniProt A0A3Q7G7F0 · UniProt A0A3Q7HSH1 · UniProt K4ATQ2 · UniProt K4CYU9 · UniProt Q38JI8 · UniProt A0A3Q7I5D6 · UniProt A0A1U8DQX3 · UniProt A0A0V0GRY5 · UniProt A0A1U7YEG5 · UniProt A0A3Q7GQ29

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