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Cryo-EM structure of the small subunit of leishmania ribosome bound to paromomycin

Analyse Cryo-EM structure of the small subunit of leishmania ribosome bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AZ1
Type: protein + RNA
Length: 6,811 residues
Chains: 38
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosomal protein S1E; Ribosomal protein S2; Ribosomal protein S3; Ribosomal protein S4…
UniProt: E9BRS2, E9BQ25, E9BTJ0, E9BBI6, E9BNF0, E9B7A8, E9BAV6, E9BH78, E9BI96, E9BTG4, E9BMA8, E9BFB6, E9BBC0, E9BTF9, E9BJV7, E9BPR7, E9BJZ5, E9BR60, E9BU11, E9BHM6, E9BK95, E9BUA2, E9BIH3, E9BLG3, E9BTC5, Q9BIJ5
Ligands: PAR, MG
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · 37 distinct chains · 28% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribosomal protein S1E	protein	225	26% helix, 29% strand	E9BRS2
B	Ribosomal protein S2	protein	211	32% helix, 14% strand	—
C	Ribosomal protein S3	protein	212	33% helix, 26% strand	E9BQ25
D	Ribosomal protein S4	protein	182	47% helix, 4% strand	E9BTJ0
E	Ribosomal protein S4E	protein	260	13% helix, 30% strand	E9BBI6
F	Ribosomal protein S5	protein	220	30% helix, 26% strand	E9BNF0
G	Ribosomal protein S6E	protein	238	27% helix, 21% strand	—
H	Ribosomal protein S7	protein	184	50% helix, 7% strand	—
I	Ribosomal protein S7E	protein	200	38% helix, 25% strand	E9B7A8
J	Ribosomal protein S8	protein	129	33% helix, 29% strand	E9BAV6
K	Ribosomal protein S8E	protein	183	23% helix, 27% strand	E9BH78
L	Ribosomal protein S9	protein	143	33% helix, 21% strand	E9BI96
M	Ribosomal protein S10	protein	102	19% helix, 42% strand	—
N	Ribosomal protein S10E	protein	91	41% helix, 22% strand	E9BTG4
O	Ribosomal protein S11	protein	137	24% helix, 25% strand	E9BMA8
P	Ribosomal protein S12	protein	142	18% helix, 28% strand	E9BFB6
Q	Ribosomal protein S12E	protein	115	27% helix, 13% strand	E9BBC0
R	Ribosomal protein S13	protein	142	44% helix, 8% strand	E9BTF9
S	Ribosomal protein S14	protein	54	30% helix, 9% strand	E9BJV7
T	Ribosomal protein S15	protein	142	56% helix, 0% strand	E9BPR7
U	Ribosomal protein S17	protein	156	0% helix, 27% strand	—
V	Ribosomal protein S17E	protein	122	55% helix, 1% strand	E9BJZ5
W	Ribosomal protein S19	protein	110	33% helix, 14% strand	—
X	Ribosomal protein S19E	protein	152	43% helix, 8% strand	E9BR60
Y	Ribosomal protein S21E	protein	88	20% helix, 23% strand	—
Z	Ribosomal protein S24E	protein	127	31% helix, 23% strand	E9BU11
a	Ribosomal protein S25E	protein	72	42% helix, 21% strand	E9BHM6
b	Ribosomal protein S26E	protein	103	17% helix, 14% strand	E9BK95
c	Ribosomal protein S27E	protein	84	7% helix, 24% strand	E9BUA2
d	Ribosomal protein S28E	protein	65	0% helix, 46% strand	E9BIH3
e	Ribosomal protein S30E	protein	59	34% helix, 0% strand	E9BLG3
f	Ribosomal protein S31E	protein	60	0% helix, 3% strand	E9BTC5
g	LACK1	protein	300	0% helix, 45% strand	Q9BIJ5
1	Ribosomal RNA 18S	rna	1760	—	—
2, 4	TRNA-phe	rna	76	—	—
3	P-site tRNA	rna	77	—	—
5	MRNA	rna	12	—	—

Ligands and binding sites

PAR · Paromomycin · ligand · 6 copies · chains 1, L, P
MG · Magnesium ion · metal · 24 copies · chains C, D, 1, S, L, b, 5

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	1006	0.90	0.93	122	empty
2	836	0.89	0.93	89	empty
3	1109	0.88	0.90	90	MG
4	753	0.87	0.91	84	empty
5	567	0.87	0.93	71	empty

Interfaces

107 interfaces between chains.

G–1 · 5526 Å² buried · 105 hydrogen bonds · protein-nucleic
E–1 · 4473 Å² buried · 88 hydrogen bonds · protein-nucleic
X–1 · 4105 Å² buried · 101 hydrogen bonds · protein-nucleic
D–1 · 3928 Å² buried · 80 hydrogen bonds · protein-nucleic
K–1 · 3837 Å² buried · 82 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 37 modified, 13 disulfide, 1 covalent (nucleotide modification, disulfide, covalent ligand).

Compared structures

6AZ1 · Cryo-EM structure of the small subunit of Leishmania ribosome bound to paromomycin · the same entry in another collection · chain B against B, 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 E9BRS2
Every structure of UniProt E9BQ25
Every structure of UniProt E9BTJ0
Every structure of UniProt E9BBI6
Every structure of UniProt E9BNF0
Every structure of UniProt E9B7A8
Every structure of UniProt E9BAV6
Every structure of UniProt E9BH78
Every structure of UniProt E9BI96
Every structure of UniProt E9BTG4
Every structure of UniProt E9BMA8
Every structure of UniProt E9BFB6
Every structure of UniProt E9BBC0
Every structure of UniProt E9BTF9
Every structure of UniProt E9BJV7
Every structure of UniProt E9BPR7
Every structure of UniProt E9BJZ5
Every structure of UniProt E9BR60
Every structure of UniProt E9BU11
Every structure of UniProt E9BHM6
Every structure of UniProt E9BK95
Every structure of UniProt E9BUA2
Every structure of UniProt E9BIH3
Every structure of UniProt E9BLG3
Every structure of UniProt E9BTC5
Every structure of UniProt Q9BIJ5
Elsewhere: RCSB PDB 6AZ1 · PDBe 6AZ1 · UniProt E9BRS2 · UniProt E9BQ25 · UniProt E9BTJ0 · UniProt E9BBI6 · UniProt E9BNF0 · UniProt E9B7A8 · UniProt E9BAV6 · UniProt E9BH78 · UniProt E9BI96 · UniProt E9BTG4 · UniProt E9BMA8 · UniProt E9BFB6 · UniProt E9BBC0 · UniProt E9BTF9 · UniProt E9BJV7 · UniProt E9BPR7 · UniProt E9BJZ5 · UniProt E9BR60 · UniProt E9BU11 · UniProt E9BHM6 · UniProt E9BK95 · UniProt E9BUA2 · UniProt E9BIH3 · UniProt E9BLG3 · UniProt E9BTC5 · UniProt Q9BIJ5

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