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Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1,3''Bz bound
Analyse Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DUJ
- 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
- Molecule
- 30S Ribosomal RNA rRNA; 30S ribosomal protein S2; 30S ribosomal protein S3; 30S ribosomal…
- UniProt
- P80371, P80372, P80373, Q5SHQ5, Q5SLP8, P17291, P0DOY9, P80374, Q5SHN7, P80376, A0A3P4AU90, P80377, P0DOY6, Q5SJ76, Q5SJH3, P24321, Q5SLQ0, Q5SHP2, P80380, Q5SIH3
- Ligands
- SIS, MG, ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · resolution 3.75 · 23 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 30S Ribosomal RNA rRNA | rna | 1512 | — | — |
| B | 30S ribosomal protein S2 | protein | 234 | 50% helix, 12% strand | P80371 |
| C | 30S ribosomal protein S3 | protein | 206 | 34% helix, 22% strand | P80372 |
| D | 30S ribosomal protein S4 | protein | 208 | 37% helix, 9% strand | P80373 |
| E | 30S ribosomal protein S5 | protein | 150 | 29% helix, 38% strand | Q5SHQ5 |
| F | 30S ribosomal protein S6 | protein | 101 | 26% helix, 49% strand | Q5SLP8 |
| G | 30S ribosomal protein S7 | protein | 155 | 55% helix, 8% strand | P17291 |
| H | 30S ribosomal protein S8 | protein | 138 | 26% helix, 34% strand | P0DOY9 |
| I | 30S ribosomal protein S9 | protein | 127 | 35% helix, 21% strand | P80374 |
| J | 30S ribosomal protein S10 | protein | 98 | 21% helix, 34% strand | Q5SHN7 |
| K | 30S ribosomal protein S11 | protein | 116 | 28% helix, 28% strand | P80376 |
| L | 30S ribosomal protein S12 | protein | 124 | 7% helix, 27% strand | A0A3P4AU90 |
| M | 30S ribosomal protein S13 | protein | 118 | 47% helix, 2% strand | P80377 |
| N | 30S ribosomal protein S14 type Z | protein | 60 | 30% helix, 8% strand | P0DOY6 |
| O | 30S ribosomal protein S15 | protein | 87 | 76% helix, 0% strand | Q5SJ76 |
| P | 30S ribosomal protein S16 | protein | 83 | 23% helix, 29% strand | Q5SJH3 |
| Q | 30S ribosomal protein S17 | protein | 99 | 15% helix, 52% strand | P24321 |
| R | 30S ribosomal protein S18 | protein | 70 | 39% helix, 9% strand | Q5SLQ0 |
| S | 30S ribosomal protein S19 | protein | 80 | 19% helix, 19% strand | Q5SHP2 |
| T | 30S ribosomal protein S20 | protein | 99 | 70% helix, 0% strand | P80380 |
| U | 30S ribosomal protein Thx | protein | 24 | 29% helix, 8% strand | Q5SIH3 |
| Y | RNA (5'-R(*UP*UP*UP*UP*UP*U)-3') | rna | 6 | — | — |
| W | RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3') | rna | 15 | — | — |
Ligands and binding sites
- SIS · (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside · ligand · chains A
- MG · Magnesium ion · metal · 249 copies · chains A, D, E, L, Q, B, C, K, P, W, N, I, U, T, J, M, S, F, H
- 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.87 | 0.90 | 88 | MG |
| 2 | 630 | 0.84 | 0.90 | 60 | MG |
| 3 | 909 | 0.84 | 0.87 | 83 | MG |
| 4 | 606 | 0.83 | 0.88 | 54 | MG |
| 5 | 520 | 0.83 | 0.90 | 44 | MG |
Interfaces
46 interfaces between chains.
- A–L · 3466 Ų buried · 92 hydrogen bonds · protein-nucleic
- A–D · 3147 Ų buried · 84 hydrogen bonds · protein-nucleic
- A–I · 2955 Ų buried · 67 hydrogen bonds · protein-nucleic
- A–T · 2823 Ų buried · 66 hydrogen bonds · protein-nucleic
- A–Q · 2784 Ų buried · 51 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 15 modified (nucleotide modification, nonstandard).
Compared structures
- 7DUJ · Crystal structure of the thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and… · the same entry in another collection · chain J against J, 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 7DUJ · PDBe 7DUJ · 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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