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Crystal structure of 30S ribosomal subunit from thermus thermophilus

Analyse Crystal structure of 30S ribosomal subunit from thermus thermophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LFC
Type: protein + RNA
Length: 3,902 residues
Chains: 21
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 16S rRNA; Ribosomal protein S2; Ribosomal protein S3; Ribosomal protein S4; Ribosomal…
UniProt: P80371, P80372, P80373, Q5SHQ5, Q5SLP8, P17291, Q5SHQ2, P80374, Q5SHN7, P80376, F6DEQ7, P80377, Q5SHQ1, Q5SJ76, Q5SJH3, Q5SHP7, Q5SLQ0, Q5SHP2, P80380, Q5SIH3
Ligands: TOY, MG, K, ZN
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 21 distinct chains · 36% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	16S rRNA	rna	1512	—	—
B	Ribosomal protein S2	protein	235	44% helix, 11% strand	P80371
C	Ribosomal protein S3	protein	206	38% helix, 22% strand	P80372
D	Ribosomal protein S4	protein	208	40% helix, 9% strand	P80373
E	Ribosomal protein S5	protein	150	29% helix, 41% strand	Q5SHQ5
F	Ribosomal protein S6	protein	101	30% helix, 49% strand	Q5SLP8
G	Ribosomal protein S7	protein	155	54% helix, 9% strand	P17291
H	Ribosomal protein S8	protein	138	27% helix, 35% strand	Q5SHQ2
I	Ribosomal protein S9	protein	127	29% helix, 21% strand	P80374
J	Ribosomal protein S10	protein	98	14% helix, 24% strand	Q5SHN7
K	Ribosomal protein S11	protein	119	26% helix, 26% strand	P80376
L	Ribosomal protein S12	protein	124	8% helix, 28% strand	F6DEQ7
M	Ribosomal protein S13	protein	118	47% helix, 2% strand	P80377
N	Ribosomal protein S14	protein	60	25% helix, 8% strand	Q5SHQ1
O	Ribosomal protein S15	protein	88	75% helix, 0% strand	Q5SJ76
P	Ribosomal protein S16	protein	83	22% helix, 30% strand	Q5SJH3
Q	Ribosomal protein S17	protein	104	15% helix, 42% strand	Q5SHP7
R	Ribosomal protein S18	protein	73	34% helix, 7% strand	Q5SLQ0
S	Ribosomal protein S19	protein	80	28% helix, 15% strand	Q5SHP2
T	Ribosomal protein S20	protein	99	73% helix, 0% strand	P80380
U	Ribosomal protein thx	protein	24	29% helix, 0% strand	Q5SIH3

Ligands and binding sites

TOY · Tobramycin · ligand · chains A
MG · Magnesium ion · metal · 133 copies · chains A, E, D, N, T, L, K, U, B, H, J, M, Q, S
K · Potassium ion · metal · 16 copies · chains A
ZN · Zinc ion · metal · 2 copies · chains D, 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	849	0.88	0.92	69	MG
2	991	0.85	0.87	95	MG
3	1094	0.85	0.87	90	MG
4	1110	0.85	0.87	98	MG
5	945	0.84	0.87	74	MG

Interfaces

41 interfaces between chains.

A–L · 3232 Å² buried · 87 hydrogen bonds · protein-nucleic
A–D · 3143 Å² buried · 86 hydrogen bonds · protein-nucleic
A–I · 2996 Å² buried · 77 hydrogen bonds · protein-nucleic
A–Q · 2707 Å² buried · 65 hydrogen bonds · protein-nucleic
A–T · 2685 Å² buried · 59 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 15 modified (nucleotide modification, nonstandard).

Compared structures

4LFC · Crystal Structure of 30S ribosomal subunit from Thermus thermophilus · the same entry in another collection · chain A against A, 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 P80371
Every structure of UniProt P80372
Every structure of UniProt P80373
Every structure of UniProt Q5SHQ5
Every structure of UniProt Q5SLP8
Every structure of UniProt P17291
Every structure of UniProt Q5SHQ2
Every structure of UniProt P80374
Every structure of UniProt Q5SHN7
Every structure of UniProt P80376
Every structure of UniProt F6DEQ7
Every structure of UniProt P80377
Every structure of UniProt Q5SHQ1
Every structure of UniProt Q5SJ76
Every structure of UniProt Q5SJH3
Every structure of UniProt Q5SHP7
Every structure of UniProt Q5SLQ0
Every structure of UniProt Q5SHP2
Every structure of UniProt P80380
Every structure of UniProt Q5SIH3
Elsewhere: RCSB PDB 4LFC · PDBe 4LFC · UniProt P80371 · UniProt P80372 · UniProt P80373 · UniProt Q5SHQ5 · UniProt Q5SLP8 · UniProt P17291 · UniProt Q5SHQ2 · UniProt P80374 · UniProt Q5SHN7 · UniProt P80376 · UniProt F6DEQ7 · UniProt P80377 · UniProt Q5SHQ1 · UniProt Q5SJ76 · UniProt Q5SJH3 · UniProt Q5SHP7 · UniProt Q5SLQ0 · UniProt Q5SHP2 · UniProt P80380 · UniProt Q5SIH3

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