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Structure of the thermus thermophilus 30S ribosomal subunit in complex with a messenger RNA fragment and cognate transfer RNA anticodon stem-loop bound at the a site

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

PDB: 1IBM
Type: protein + RNA
Length: 3,924 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 16S ribosomal RNA; P-site messenger RNA fragment; Anticodon stem-loop of phenylalanine…
UniProt: P80373, P27152, P23370, P17291, P24319, P80375, P17293, P24320, P80378, P80381, P32193
Ligands: MG, ZN
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 24 distinct chains · 35% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	16S ribosomal RNA	rna	1507	—	—
X	P-site messenger RNA fragment	rna	6	—	—
Y	Anticodon stem-loop of phenylalanine transfer RNA	rna	11	—	—
Z	A-site messenger RNA fragment	rna	4	—	—
B	30S ribosomal protein S2	protein	234	46% helix, 11% strand	—
C	30S ribosomal protein S3	protein	206	32% helix, 14% strand	—
D	30S ribosomal protein S4	protein	208	38% helix, 6% strand	P80373
E	30S ribosomal protein S5	protein	150	28% helix, 35% strand	P27152
F	30S ribosomal protein S6	protein	101	28% helix, 46% strand	P23370
G	30S ribosomal protein S7	protein	155	51% helix, 6% strand	P17291
H	30S ribosomal protein S8	protein	138	28% helix, 28% strand	P24319
I	30S ribosomal protein S9	protein	127	35% helix, 16% strand	—
J	30S ribosomal protein S10	protein	98	20% helix, 18% strand	P80375
K	30S ribosomal protein S11	protein	119	28% helix, 25% strand	—
L	30S ribosomal protein S12	protein	124	5% helix, 19% strand	P17293
M	30S ribosomal protein S13	protein	118	50% helix, 0% strand	—
N	30S ribosomal protein S14	protein	60	22% helix, 7% strand	P24320
O	30S ribosomal protein S15	protein	88	74% helix, 0% strand	P80378
P	30S ribosomal protein S16	protein	83	20% helix, 29% strand	—
Q	30S ribosomal protein S17	protein	104	13% helix, 40% strand	—
R	30S ribosomal protein S18	protein	73	33% helix, 8% strand	—
S	30S ribosomal protein S19	protein	87	20% helix, 15% strand	P80381
T	30S ribosomal protein S20	protein	99	72% helix, 0% strand	—
V	30S ribosomal protein thx	protein	24	25% helix, 8% strand	P32193

Ligands and binding sites

MG · Magnesium ion · metal · 120 copies · chains A, E, N, C, V, H, D, L, Q, T, Z, X, J
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	1036	0.89	0.91	87	MG
2	638	0.85	0.90	66	MG
3	1193	0.83	0.84	88	MG
4	1023	0.83	0.85	77	empty
5	693	0.83	0.88	56	MG

Interfaces

47 interfaces between chains.

A–L · 3266 Å² buried · 87 hydrogen bonds · protein-nucleic
A–I · 2990 Å² buried · 93 hydrogen bonds · protein-nucleic
A–D · 2980 Å² buried · 94 hydrogen bonds · protein-nucleic
A–Q · 2760 Å² buried · 63 hydrogen bonds · protein-nucleic
A–T · 2588 Å² buried · 66 hydrogen bonds · protein-nucleic

Compared structures

1IBM · Structure of the thermus thermophilus 30S ribosomal subunit in complex with a messenger… · 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 P80375
Every structure of UniProt P17293
Every structure of UniProt P24320
Every structure of UniProt P80378
Every structure of UniProt P80381
Every structure of UniProt P32193
Elsewhere: RCSB PDB 1IBM · PDBe 1IBM · UniProt P80373 · UniProt P27152 · UniProt P23370 · UniProt P17291 · UniProt P24319 · UniProt P80375 · UniProt P17293 · UniProt P24320 · UniProt P80378 · UniProt P80381 · UniProt P32193

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