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Crystal Structure of the 30S ribosomal subunit from a KsgA mutant of Thermus thermophilus (HB8)

Analyse Crystal Structure of the 30S ribosomal subunit from a KsgA mutant of Thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3OTO
Type: protein + RNA
Length: 3,900 residues
Chains: 21
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.69
Source: Thermus thermophilus
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, P80379, P24321, P80382, P80381, P80380, P32193
Ligands: MG, K, ZN
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · resolution 3.69 · 21 distinct chains · 33% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	16S rRNA	rna	1513	—	—
B	30S ribosomal protein S2	protein	235	38% helix, 13% strand	—
C	30S ribosomal protein S3	protein	206	28% helix, 22% strand	—
D	30S ribosomal protein S4	protein	208	40% helix, 7% strand	P80373
E	30S ribosomal protein S5	protein	150	27% helix, 37% strand	P27152
F	30S ribosomal protein S6	protein	101	32% helix, 36% strand	P23370
G	30S ribosomal protein S7	protein	155	46% helix, 5% strand	P17291
H	30S ribosomal protein S8	protein	138	29% helix, 30% strand	P24319
I	30S ribosomal protein S9	protein	127	29% helix, 21% strand	—
J	30S ribosomal protein S10	protein	98	7% helix, 20% strand	P80375
K	30S ribosomal protein S11	protein	119	26% helix, 28% strand	—
L	30S ribosomal protein S12	protein	124	11% helix, 19% strand	P17293
M	30S ribosomal protein S13	protein	115	50% helix, 2% strand	—
N	30S ribosomal protein S14	protein	60	20% helix, 3% strand	P24320
O	30S ribosomal protein S15	protein	88	72% helix, 0% strand	P80378
P	30S ribosomal protein S16	protein	83	20% helix, 23% strand	P80379
Q	30S ribosomal protein S17	protein	104	14% helix, 37% strand	P24321
R	30S ribosomal protein S18	protein	73	34% helix, 8% strand	P80382
S	30S ribosomal protein S19	protein	80	21% helix, 15% strand	P80381
T	30S ribosomal protein S20	protein	99	73% helix, 0% strand	P80380
U	30S ribosomal protein thx	protein	24	17% helix, 0% strand	P32193

Ligands and binding sites

MG · Magnesium ion · metal · 94 copies · chains A, K, L, E, N, T, D, J, U, B, M
K · Potassium ion · metal · 42 copies · chains A, I, E
ZN · Zinc ion · metal · 2 copies · chains D, A, 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	997	0.89	0.92	88	MG, K
2	1093	0.86	0.88	102	MG
3	1105	0.85	0.87	90	MG, K
4	836	0.84	0.87	83	MG
5	584	0.83	0.89	62	MG, K

Interfaces

42 interfaces between chains.

A–L · 3174 Å² buried · 88 hydrogen bonds · protein-nucleic
A–D · 3103 Å² buried · 89 hydrogen bonds · protein-nucleic
A–I · 2963 Å² buried · 88 hydrogen bonds · protein-nucleic
A–Q · 2864 Å² buried · 61 hydrogen bonds · protein-nucleic
A–T · 2690 Å² buried · 63 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

3OTO · Crystal structure of the 30S ribosomal subunit from a ksga mutant of thermus thermophilus… · the same entry in another collection · chain K against K, 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 P80379
Every structure of UniProt P24321
Every structure of UniProt P80382
Every structure of UniProt P80381
Every structure of UniProt P80380
Every structure of UniProt P32193
Elsewhere: RCSB PDB 3OTO · PDBe 3OTO · UniProt P80373 · UniProt P27152 · UniProt P23370 · UniProt P17291 · UniProt P24319 · UniProt P80375 · UniProt P17293 · UniProt P24320 · UniProt P80378 · UniProt P80379 · UniProt P24321 · UniProt P80382 · UniProt P80381 · UniProt P80380 · UniProt P32193

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