MolNFT v1 · #6686 · protein + RNA

Structure of functionally activated small ribosomal subunit at 3.3 a resolution

1FKA · 16S ribosomal RNA: “Structure of functionally activated small ribosomal subunit at 3.3 a resolution”. X-ray diffraction, 1 ligand (WO2), 20 pockets (best druggability 0.82). MolNFT v1 #6686 on GenesisL1: 3D structure, binding sites…

PDB: 1FKA
Type: protein + RNA
Length: 3,343 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 16S ribosomal RNA; 30S ribosomal protein S2; 30S ribosomal protein S3; 30S ribosomal…
UniProt: P80373, P27152, P23370, P17291, P24319, P80378, P80381
Ligands: WO2
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 19 distinct chains · 21% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	16S ribosomal RNA	rna	1479	—	—
B	30S ribosomal protein S2	protein	111	0% helix, 0% strand	—
C	30S ribosomal protein S3	protein	176	0% helix, 0% strand	—
D	30S ribosomal protein S4	protein	161	38% helix, 11% strand	P80373
E	30S ribosomal protein S5	protein	157	19% helix, 25% strand	P27152
F	30S ribosomal protein S6	protein	97	28% helix, 28% strand	P23370
G	30S ribosomal protein S7	protein	128	59% helix, 2% strand	P17291
H	30S ribosomal protein S8	protein	136	24% helix, 26% strand	P24319
I	30S ribosomal protein S9	protein	89	0% helix, 0% strand	—
J, K	30S ribosomal protein S10	protein	70	0% helix, 0% strand	—
L	30S ribosomal protein S12	protein	103	0% helix, 0% strand	—
M	30S ribosomal protein S13	protein	77	0% helix, 0% strand	—
N	30S ribosomal protein S14	protein	26	0% helix, 0% strand	—
O	30S ribosomal protein S15	protein	88	70% helix, 0% strand	P80378
P	30S ribosomal protein S16	protein	73	0% helix, 0% strand	—
Q	30S ribosomal protein S17	protein	84	20% helix, 2% strand	—
R	30S ribosomal protein S18	protein	50	22% helix, 0% strand	—
S	30S ribosomal protein S19	protein	73	16% helix, 5% strand	P80381
T	30S ribosomal protein S20	protein	95	53% helix, 0% strand	—

Ligands and binding sites

WO2 · Octadecatungstenyl diphosphate · metal · 7 copies

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	1122	0.82	0.84	113	empty
2	921	0.81	0.84	87	empty
3	576	0.81	0.87	81	empty
4	721	0.80	0.85	63	empty
5	697	0.79	0.84	87	empty

Interfaces

26 interfaces between chains.

A–H · 1080 Å² buried · 8 hydrogen bonds · protein-nucleic
A–O · 957 Å² buried · 12 hydrogen bonds · protein-nucleic
A–T · 861 Å² buried · 3 hydrogen bonds · protein-nucleic
A–I · 851 Å² buried · 0 hydrogen bonds · protein-nucleic
A–P · 773 Å² buried · 0 hydrogen bonds · protein-nucleic

Compared structures

1FKA · Structure of functionally activated small ribosomal subunit at 3.3 a resolution · the same entry in another collection · chain H against H, 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 P80378
Every structure of UniProt P80381
Elsewhere: RCSB PDB 1FKA · PDBe 1FKA · UniProt P80373 · UniProt P27152 · UniProt P23370 · UniProt P17291 · UniProt P24319 · UniProt P80378 · UniProt P80381

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