MolNFT v1 · #15385 · protein + RNA

Structure of the thermus thermophilus 30S ribosomal subunit in the presence of crystallographically disordered codon and near-cognate transfer RNA anticodon stem-loop mismatched at the second codon position

1N36 · 16S ribosomal RNA: “Structure of the thermus thermophilus 30S ribosomal subunit in the presence of crystallographically…”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.88). MolNFT v1 #15385 on GenesisL1: 3D…

PDB: 1N36
Type: protein + RNA
Length: 3,902 residues
Chains: 21
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: P80371, P80372, P80373, Q5SHQ5, Q5SLP8, P17291, Q5SHQ2, P80374, Q5SHN7, P80376, Q5SHN3, P80377, Q5SHQ1, Q5SJ76, Q5SJH3, Q5SHP7, Q5SLQ0, Q5SHP2, P80380
Ligands: ZN
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 21 distinct chains · 31% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	16S ribosomal RNA	rna	1513	—	—
B	30S ribosomal protein S2	protein	234	37% helix, 9% strand	P80371
C	30S ribosomal protein S3	protein	206	26% helix, 6% strand	P80372
D	30S ribosomal protein S4	protein	208	38% helix, 4% strand	P80373
E	30S ribosomal protein S5	protein	150	33% helix, 31% strand	Q5SHQ5
F	30S ribosomal protein S6	protein	101	15% helix, 27% strand	Q5SLP8
G	30S ribosomal protein S7	protein	155	44% helix, 5% strand	P17291
H	30S ribosomal protein S8	protein	138	30% helix, 19% strand	Q5SHQ2
I	30S ribosomal protein S9	protein	127	25% helix, 6% strand	P80374
J	30S ribosomal protein S10	protein	98	15% helix, 12% strand	Q5SHN7
K	30S ribosomal protein S11	protein	119	28% helix, 17% strand	P80376
L	30S ribosomal protein S12	protein	124	4% helix, 14% strand	Q5SHN3
M	30S ribosomal protein S13	protein	118	45% helix, 0% strand	P80377
N	30S ribosomal protein S14	protein	60	13% helix, 2% strand	Q5SHQ1
O	30S ribosomal protein S15	protein	88	74% helix, 0% strand	Q5SJ76
P	30S ribosomal protein S16	protein	83	22% helix, 13% strand	Q5SJH3
Q	30S ribosomal protein S17	protein	104	14% helix, 38% strand	Q5SHP7
R	30S ribosomal protein S18	protein	73	38% helix, 5% strand	Q5SLQ0
S	30S ribosomal protein S19	protein	80	13% helix, 8% strand	Q5SHP2
T	30S ribosomal protein S20	protein	99	69% helix, 0% strand	P80380
V	30S ribosomal protein thx	protein	24	25% helix, 0% strand	P80380

Ligands and binding sites

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	1049	0.88	0.91	87	empty
2	959	0.85	0.87	96	empty
3	849	0.84	0.88	64	empty
4	532	0.84	0.90	55	empty
5	644	0.83	0.89	65	empty

Interfaces

41 interfaces between chains.

A–L · 3167 Å² buried · 84 hydrogen bonds · protein-nucleic
A–D · 2933 Å² buried · 82 hydrogen bonds · protein-nucleic
A–I · 2880 Å² buried · 74 hydrogen bonds · protein-nucleic
A–Q · 2785 Å² buried · 65 hydrogen bonds · protein-nucleic
A–P · 2633 Å² buried · 52 hydrogen bonds · protein-nucleic

Compared structures

1N36 · Structure of the Thermus thermophilus 30S ribosomal subunit in the presence of… · the same entry in another collection · chain B against B, 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 Q5SHN3
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
Elsewhere: RCSB PDB 1N36 · PDBe 1N36 · UniProt P80371 · UniProt P80372 · UniProt P80373 · UniProt Q5SHQ5 · UniProt Q5SLP8 · UniProt P17291 · UniProt Q5SHQ2 · UniProt P80374 · UniProt Q5SHN7 · UniProt P80376 · UniProt Q5SHN3 · UniProt P80377 · UniProt Q5SHQ1 · UniProt Q5SJ76 · UniProt Q5SJH3 · UniProt Q5SHP7 · UniProt Q5SLQ0 · UniProt Q5SHP2 · UniProt P80380

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.