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Crystal structures of the small ribosomal subunit with tetracycline, edeine and IF3

Analyse Crystal structures of the small ribosomal subunit with tetracycline, edeine and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1I94
Type: protein + RNA
Length: 3,924 residues
Chains: 21
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 16S rRNA; 30S ribosomal protein S2; 30S ribosomal protein S3; 30S ribosomal protein S4…
UniProt: P80373, P27152, P23370, P17291, P24319, P80375, P17293, P24320, P80378, P24321, P80381
Ligands: WO2, MG, ZN
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 21 distinct chains · 32% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	16S rRNA	rna	1514	—	—
B	30S ribosomal protein S2	protein	249	35% helix, 4% strand	—
C	30S ribosomal protein S3	protein	206	30% helix, 18% strand	—
D	30S ribosomal protein S4	protein	208	38% helix, 8% strand	P80373
E	30S ribosomal protein S5	protein	156	25% helix, 24% strand	P27152
F	30S ribosomal protein S6	protein	101	28% helix, 30% strand	P23370
G	30S ribosomal protein S7	protein	155	50% helix, 3% strand	P17291
H	30S ribosomal protein S8	protein	138	26% helix, 25% strand	P24319
I	30S ribosomal protein S9	protein	127	29% helix, 13% strand	—
J	30S ribosomal protein S10	protein	98	15% helix, 32% strand	P80375
K	30S ribosomal protein S11	protein	123	21% helix, 24% strand	—
L	30S ribosomal protein S12	protein	131	4% helix, 19% strand	P17293
M	30S ribosomal protein S13	protein	93	53% helix, 0% strand	—
N	30S ribosomal protein S14	protein	60	23% helix, 10% strand	P24320
O	30S ribosomal protein S15	protein	88	70% helix, 0% strand	P80378
P	30S ribosomal protein S16	protein	88	23% helix, 15% strand	—
Q	30S ribosomal protein S17	protein	104	13% helix, 32% strand	P24321
R	30S ribosomal protein S18	protein	82	23% helix, 2% strand	—
S	30S ribosomal protein S19	protein	80	21% helix, 15% strand	P80381
T	30S ribosomal protein S20	protein	99	71% helix, 0% strand	—
U	30S ribosomal protein thx	protein	24	21% helix, 8% strand	—

Ligands and binding sites

WO2 · Octadecatungstenyl diphosphate · ligand · 14 copies · chains B, A, C, E, H, G, K, R, J, D, T
MG · Magnesium ion · metal · 75 copies · chains A, E, L, T, Q, P, D, K, G, N, J
ZN · Zinc ion · metal · 2 copies · chains N, D

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	1109	0.88	0.91	132	MG
2	1031	0.86	0.88	130	MG
3	884	0.84	0.87	126	MG
4	585	0.81	0.87	86	empty
5	552	0.81	0.88	46	MG

Interfaces

36 interfaces between chains.

A–L · 1799 Å² buried · 22 hydrogen bonds · protein-nucleic
A–D · 1571 Å² buried · 17 hydrogen bonds · protein-nucleic
A–I · 1513 Å² buried · 24 hydrogen bonds · protein-nucleic
A–Q · 1435 Å² buried · 17 hydrogen bonds · protein-nucleic
A–P · 1321 Å² buried · 14 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 5 covalent (covalent ligand).

Compared structures

1I94 · Crystal structures of the small ribosomal subunit with tetracycline, edeine and IF3 · the same entry in another collection · chain J against J, 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 P80373
Every structure of UniProt P27152
Every structure of UniProt P23370
Every structure of UniProt P17291
Every structure of UniProt P24319
Every structure of UniProt P80375
Every structure of UniProt P17293
Every structure of UniProt P24320
Every structure of UniProt P80378
Every structure of UniProt P24321
Every structure of UniProt P80381
Elsewhere: RCSB PDB 1I94 · PDBe 1I94 · UniProt P80373 · UniProt P27152 · UniProt P23370 · UniProt P17291 · UniProt P24319 · UniProt P80375 · UniProt P17293 · UniProt P24320 · UniProt P80378 · UniProt P24321 · UniProt P80381

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