GL1X · GenesisL1 explorer

MolNFT v2 · #158839 · protein + RNA

Crystal structure of the Thermus thermophilus 70S ribosome in complex with a short substrate mimic CC-Pmn and bound to mRNA and P-site tRNA at 3.7A resolution

6N9E: “Crystal structure of the Thermus thermophilus 70S ribosome in complex with a short substrate mimic CC-Pmn and…”. X-ray diffraction at 3.7, 3 ligands (SF4, MG, ZN). MolNFT v2 #158839 on GenesisL1: 3D structure, binding sites and…

PDB
6N9E
Type
protein + RNA
Length
20,651 residues
Chains
110
Method
x-ray diffraction
Collection
MolNFT v2 / PDB Bank
Contract
0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner
0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution
3.7
Source
Escherichia coli; Thermus thermophilus; SYNTHETIC CONSTRUCT
UniProt
Q56435, Q72IA7, P60493, P60494, Q72I12, P74909, Q72JR0, P80339, Q72GW3, P80340, P80374, P80375, P62654, P17293, P62655, P24320, P80378, P62238, P0DOY7, P62659, P62612
Ligands
SF4, MG, ZN

Structure

x-ray diffraction · resolution 3.7 · 60 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
1A—rna2871——
1B, 2B—rna120——
1D, 2D—protein275——
1E, 2E—protein204——
1F, 2F—protein202——
1G, 2G—protein181——
1H, 2H—protein174——
1I, 2I—protein146——
1N, 2N—protein140——
1O, 2O—protein122——
1P, 2P—protein149——
1Q, 2Q—protein141——
1R, 2R—protein118——
1S, 2S—protein110——
1T, 2T—protein131——
1U, 2U—protein116——
1V, 2V—protein101——
1W, 2W—protein112——
1X, 2X—protein95——
1Y, 2Y—protein107—Q56435
1Z—protein154—Q72IA7
10, 20—protein83—P60493
11, 21—protein97—P60494
12, 22—protein70—Q72I12
13, 23—protein59—P74909
14, 24—protein69—Q72JR0
15, 25—protein59—P80339
16, 26—protein53—Q72GW3
17, 27—protein48—P80340
18, 28—protein64——
19, 29—protein37——
1a—rna1499——
1b, 2b—protein231——
1c, 2c—protein206——
1d, 2d—protein208——
1e, 2e—protein148——
1f, 2f—protein100——
1g, 2g—protein155——
1h, 2h—protein137——
1i, 2i—protein127—P80374
1j—protein97—P80375
1k, 2k—protein114—P62654
1l, 2l—protein122—P17293
1m—protein123—P62655
1n, 2n—protein60—P24320
1o, 2o—protein88—P80378
1p, 2p—protein82—P62238
1q, 2q—protein99—P0DOY7
1r, 2r—protein68—P62659
1s, 2s—protein83——
1t, 2t—protein96——
1u, 2u—protein23—P62612
1v, 2v—rna5——
1w, 2w—rna2——
1x, 2x—rna76——
2A—rna2800——
2Z—protein160—Q72IA7
2a—rna1503——
2j—protein96—P80375
2m—protein122—P62655

Ligands and binding sites

  • SF4 · Iron/sulfur cluster · ligand · 2 copies · chains 1d, 2d
  • MG · Magnesium ion · metal · 1156 copies · chains 1A, 1D, 1P, 1F, 13, 1V, 1B, 1R, 1Y, 1T, 1X, 1E, 1U, 18, 1N, 1a, 1S, 1W, 10, 15, 16, 17, 1t, 1q, 1u, 1h, 1l, 1i, 1d, 1m, 1r, 1x, 2A, 2P, 2F, 2D, 28, 2W, 2X, 2a, 2E, 2R, 2U, 2V, 2B, 2T, 2O, 2Q, 25, 2Y, 20, 21, 23, 2i, 2c, 2k, 2p, 2d, 2f, 2l, 2r
  • ZN · Zinc ion · metal · 12 copies · chains 1Y, 14, 15, 16, 19, 1n, 2Y, 24, 25, 26, 29, 2n

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Compared structures

  • P62238 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S16 (P62238) · a predicted model of the same protein · chain 1p against A, TM-score 0.97
  • P80378 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S15 (P80378) · a predicted model of the same protein · chain 1o against A, TM-score 0.96

Analyse

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