MolNFT v2 · #178854 · protein + RNA
Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1''AC bound
7DUH: “Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA…”. X-ray diffraction at 3.75, 3 ligands (HJO, MG, ZN). MolNFT v2 #178854 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7DUH
- Type
- protein + RNA
- Length
- 3,910 residues
- Chains
- 23
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.75
- Source
- Thermus thermophilus; Thermus thermophilus HB8
- UniProt
- P80371, P80372, P80373, Q5SHQ5, Q5SLP8, P17291, P0DOY9, P80374, Q5SHN7, P80376, A0A3P4AU90, P80377, P0DOY6, Q5SJ76, Q5SJH3, P24321, Q5SLQ0, Q5SHP2, P80380, Q5SIH3
- Ligands
- HJO, MG, ZN
Structure
x-ray diffraction · resolution 3.75 · 23 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | rna | 1512 | — | — |
| B | — | protein | 234 | — | P80371 |
| C | — | protein | 206 | — | P80372 |
| D | — | protein | 208 | — | P80373 |
| E | — | protein | 150 | — | Q5SHQ5 |
| F | — | protein | 101 | — | Q5SLP8 |
| G | — | protein | 155 | — | P17291 |
| H | — | protein | 138 | — | P0DOY9 |
| I | — | protein | 127 | — | P80374 |
| J | — | protein | 98 | — | Q5SHN7 |
| K | — | protein | 116 | — | P80376 |
| L | — | protein | 124 | — | A0A3P4AU90 |
| M | — | protein | 118 | — | P80377 |
| N | — | protein | 60 | — | P0DOY6 |
| O | — | protein | 87 | — | Q5SJ76 |
| P | — | protein | 83 | — | Q5SJH3 |
| Q | — | protein | 99 | — | P24321 |
| R | — | protein | 70 | — | Q5SLQ0 |
| S | — | protein | 80 | — | Q5SHP2 |
| T | — | protein | 99 | — | P80380 |
| U | — | protein | 24 | — | Q5SIH3 |
| Y | — | rna | 6 | — | — |
| W | — | rna | 15 | — | — |
Ligands and binding sites
- HJO · N-[(1R,2R,3R,4S,5S)-4-[(2R,3R,6S)-6-(aminomethyl)-3-azanyl-oxan-2-yl]oxy-5-azanyl-2-[(2R,3R,4R)-5-methyl-4-(methylamino)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]ethanamide · ligand · chains A
- MG · Magnesium ion · metal · 249 copies · chains A, Q, E, C, P, W, N, U, T, J, D, K, I, B, F, H, S
- ZN · Zinc ion · metal · 2 copies · chains D, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 7DUH · Crystal structure of the thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and… · the same entry in another collection · chain Y against Y, 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 P0DOY9
- Every structure of UniProt P80374
- Every structure of UniProt Q5SHN7
- Every structure of UniProt P80376
- Every structure of UniProt A0A3P4AU90
- Every structure of UniProt P80377
- Every structure of UniProt P0DOY6
- Every structure of UniProt Q5SJ76
- Every structure of UniProt Q5SJH3
- Every structure of UniProt P24321
- Every structure of UniProt Q5SLQ0
- Every structure of UniProt Q5SHP2
- Every structure of UniProt P80380
- Every structure of UniProt Q5SIH3
- Elsewhere: RCSB PDB 7DUH · PDBe 7DUH · UniProt P80371 · UniProt P80372 · UniProt P80373 · UniProt Q5SHQ5 · UniProt Q5SLP8 · UniProt P17291 · UniProt P0DOY9 · UniProt P80374 · UniProt Q5SHN7 · UniProt P80376 · UniProt A0A3P4AU90 · UniProt P80377 · UniProt P0DOY6 · UniProt Q5SJ76 · UniProt Q5SJH3 · UniProt P24321 · UniProt Q5SLQ0 · UniProt Q5SHP2 · UniProt P80380 · UniProt Q5SIH3
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