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MolNFT v2 · #117094 · protein + RNA

Crystal structure of the Thermus thermophilus 70S ribosome in complex with Hygromycin-A at 3.1A resolution

5DOX: “Crystal structure of the Thermus thermophilus 70S ribosome in complex with Hygromycin-A at 3.1A resolution”. X-ray diffraction at 3.1, 4 ligands (HGR, SF4, MG). MolNFT v2 #117094 on GenesisL1: 3D structure, binding sites and pockets…

PDB
5DOX
Type
protein + RNA
Length
20,617 residues
Chains
104
Method
x-ray diffraction
Collection
MolNFT v2 / PDB Bank
Contract
0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner
0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution
3.1
Source
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579); Thermus thermophilus…
UniProt
P60405, Q5SHN8, Q5SHN9, Q5SHQ0, Q5SHQ3, Q5SLQ1, P60488, Q5SHP8, Q5SHQ7, P60489, Q9Z9H5, Q5SHQ4, P60490, P60491, P60492, Q5SHP3, Q5SHP0, Q5SHP9, Q5SHZ1, P60493, P60494, Q5SHP6, Q5SHQ6, Q5SJE1, P80339, P35871, P80340, Q5SKU1, Q5SHR2, P80371, P80372, P80373, Q5SHQ5, Q5SLP8, P17291, Q5SHQ2, P80374, Q5SHN7, P80376, Q5SHN3, P80377, Q5SHQ1, Q5SJ76, Q5SJH3, Q5SHP7, Q5SLQ0, Q5SHP2, P80380, Q5SIH3
Ligands
HGR, SF4, MG, ZN

Structure

x-ray diffraction · resolution 3.1 · 61 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
1A—rna2872——
1B, 2B—rna120——
1D, 2D—protein275—P60405
1E, 2E—protein204—Q5SHN8
1F, 2F—protein202—Q5SHN9
1G, 2G—protein181—Q5SHQ0
1H—protein174—Q5SHQ3
1I—protein147—Q5SLQ1
1N, 2N—protein140—P60488
1O, 2O—protein122—Q5SHP8
1P, 2P—protein149—Q5SHQ7
1Q, 2Q—protein141—P60489
1R, 2R—protein118—Q9Z9H5
1S, 2S—protein110—Q5SHQ4
1T, 2T—protein131—P60490
1U, 2U—protein116—P60491
1V, 2V—protein101—P60492
1W, 2W—protein112—Q5SHP3
1X, 2X—protein95—Q5SHP0
1Y, 2Y—protein107—Q5SHP9
1Z—protein203—Q5SHZ1
10, 20—protein77—P60493
11, 21—protein97—P60494
12, 22—protein70—Q5SHP6
13, 23—protein59—Q5SHQ6
14, 24—protein69—Q5SJE1
15, 25—protein59—P80339
16, 26—protein53—P35871
17, 27—protein48—P80340
18, 28—protein64—Q5SKU1
19, 29—protein37—Q5SHR2
1a—rna1499——
1b, 2b—protein231—P80371
1c, 2c—protein206—P80372
1d, 2d—protein208—P80373
1e, 2e—protein148—Q5SHQ5
1f, 2f—protein100—Q5SLP8
1g, 2g—protein155—P17291
1h, 2h—protein137—Q5SHQ2
1i—protein127—P80374
1j—protein97—Q5SHN7
1k, 2k—protein114—P80376
1l, 2l—protein122—Q5SHN3
1m—protein116—P80377
1n, 2n—protein60—Q5SHQ1
1o, 2o—protein88—Q5SJ76
1p, 2p—protein82—Q5SJH3
1q, 2q—protein99—Q5SHP7
1r, 2r—protein68—Q5SLQ0
1s, 2s—protein83—Q5SHP2
1t—protein96—P80380
1u, 2u—protein23—Q5SIH3
2A—rna2867——
2H—protein173—Q5SHQ3
2I—protein146—Q5SLQ1
2Z—protein201—Q5SHZ1
2a—rna1503——
2i—protein126—P80374
2j—protein96—Q5SHN7
2m—protein114—P80377
2t—protein98—P80380

Ligands and binding sites

  • HGR · Hygromycin A · ligand · 2 copies · chains 1A, 2A
  • SF4 · Iron/sulfur cluster · ligand · 2 copies · chains 1d, 2d
  • MG · Magnesium ion · metal · 1718 copies · chains 1A, 12, 1Q, 1Z, 1U, 1R, 1F, 11, 1P, 1N, 1E, 1X, 1W, 1D, 1a, 17, 1V, 19, 1B, 1Y, 10, 15, 1G, 1H, 1T, 13, 18, 16, 1q, 1o, 1u, 1p, 1n, 1m, 1l, 1e, 1b, 1d, 1f, 1g, 1h, 1k, 1r, 1t, 2A, 2T, 29, 2W, 25, 2R, 2P, 2V, 2X, 2D, 2N, 2U, 2F, 2E, 2B, 2a, 2I, 2O, 2Q, 2Y, 20, 26, 28, 2t, 2p, 2e, 2q, 2h, 2k, 2l
  • 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

  • P60405 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L2 (P60405) · a predicted model of the same protein · chain 1D against A, TM-score 0.99
  • P60488 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L13 (P60488) · a predicted model of the same protein · chain 1N against A, TM-score 0.99
  • P60493 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L27 (P60493) · a predicted model of the same protein · chain 10 against A, TM-score 0.95
  • Q5SLQ1 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L9 (Q5SLQ1) · a predicted model of the same protein · chain 1I against A, TM-score 0.94
  • Q5SHR2 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L36 (Q5SHR2) · a predicted model of the same protein · chain 19 against A, TM-score 0.93
  • P60494 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L28 (P60494) · a predicted model of the same protein · chain 11 against A, TM-score 0.89
  • P35871 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L33 (P35871) · a predicted model of the same protein · chain 16 against A, TM-score 0.88
  • Q5SJE1 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L31 (Q5SJE1) · a predicted model of the same protein · chain 14 against A, TM-score 0.66

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