MolNFT v2 · #51099 · protein + RNA
Crystal structure of an extended tRNA anticodon stem loop in complex with its cognate mRNA GGGU in the context of the Thermus thermophilus 30S subunit.
2UXB · 16S ribosomal RNA: “Crystal structure of an extended tRNA anticodon stem loop in complex with its cognate mRNA GGGU in the…”. X-ray diffraction at 3.1, 4 ligands (PAR, MG, K), 20 pockets (best druggability 0.89). MolNFT v2 #51099 on…
- PDB
- 2UXB
- Type
- protein + RNA
- Length
- 3,920 residues
- Chains
- 23
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.1
- Source
- THERMUS THERMOPHILUS; SYNTHETIC CONSTRUCT
- Molecule
- 16S ribosomal RNA; Ribosomal protein S2; Ribosomal protein S3; Ribosomal protein S4…
- UniProt
- P80371, P80372, P80373, Q5SHQ5, Q5SLP8, P17291, Q5SHQ2, P80374, Q5SHN7, P80376, Q5SHN3, P80377, Q5SHQ1, Q5SJ76, Q5SJH3, Q5SHP7, Q5SLQ0, Q5SHP2, P80380, Q5SIH3
- Ligands
- PAR, MG, K, ZN
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · resolution 3.1 · 23 distinct chains · 32% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S ribosomal RNA | rna | 1513 | — | — |
| B | Ribosomal protein S2 | protein | 234 | 43% helix, 9% strand | P80371 |
| C | Ribosomal protein S3 | protein | 206 | 26% helix, 14% strand | P80372 |
| D | Ribosomal protein S4 | protein | 208 | 40% helix, 4% strand | P80373 |
| E | Ribosomal protein S5 | protein | 150 | 29% helix, 31% strand | Q5SHQ5 |
| F | Ribosomal protein S6 | protein | 101 | 25% helix, 35% strand | Q5SLP8 |
| G | Ribosomal protein S7 | protein | 155 | 52% helix, 4% strand | P17291 |
| H | Ribosomal protein S8 | protein | 138 | 30% helix, 27% strand | Q5SHQ2 |
| I | Ribosomal protein S9 | protein | 127 | 27% helix, 18% strand | P80374 |
| J | Ribosomal protein S10 | protein | 98 | 9% helix, 22% strand | Q5SHN7 |
| K | Ribosomal protein S11 | protein | 119 | 27% helix, 28% strand | P80376 |
| L | Ribosomal protein S12 | protein | 124 | 6% helix, 14% strand | Q5SHN3 |
| M | Ribosomal protein S13 | protein | 125 | 43% helix, 0% strand | P80377 |
| N | Ribosomal protein S14 | protein | 60 | 13% helix, 5% strand | Q5SHQ1 |
| O | Ribosomal protein S15 | protein | 88 | 70% helix, 0% strand | Q5SJ76 |
| P | Ribosomal protein S16 | protein | 83 | 16% helix, 33% strand | Q5SJH3 |
| Q | Ribosomal protein S17 | protein | 104 | 14% helix, 38% strand | Q5SHP7 |
| R | Ribosomal protein S18 | protein | 73 | 32% helix, 8% strand | Q5SLQ0 |
| S | Ribosomal protein S19 | protein | 80 | 18% helix, 10% strand | Q5SHP2 |
| T | Ribosomal protein S20 | protein | 99 | 75% helix, 0% strand | P80380 |
| U | Ribosomal protein thx | protein | 24 | 25% helix, 0% strand | Q5SIH3 |
| X | A-site messenger RNA fragment gggu | rna | 4 | — | — |
| Y | Anticodon stem-loop of transfer RNA with anticodon accc | rna | 7 | — | — |
Ligands and binding sites
- PAR · Paromomycin · ligand · chains A
- MG · Magnesium ion · metal · 131 copies · chains A, E, N, U, L, T, J, M, C, O, Q, H
- K · Potassium ion · metal · 10 copies · chains A, E
- 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.89 | 0.91 | 92 | MG |
| 2 | 1050 | 0.85 | 0.87 | 79 | MG |
| 3 | 753 | 0.85 | 0.89 | 77 | MG |
| 4 | 467 | 0.84 | 0.92 | 65 | MG |
| 5 | 843 | 0.84 | 0.87 | 69 | MG |
Interfaces
46 interfaces between chains.
- A–L · 3368 Ų buried · 84 hydrogen bonds · protein-nucleic
- A–D · 3109 Ų buried · 94 hydrogen bonds · protein-nucleic
- A–I · 3044 Ų buried · 97 hydrogen bonds · protein-nucleic
- A–Q · 2873 Ų buried · 76 hydrogen bonds · protein-nucleic
- A–T · 2656 Ų buried · 63 hydrogen bonds · protein-nucleic
Compared structures
- 2UXB · Crystal structure of an extended tRNA anticodon stem loop in complex with its cognate… · the same entry in another collection · chain K against K, 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
- Every structure of UniProt Q5SIH3
- Elsewhere: RCSB PDB 2UXB · PDBe 2UXB · 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 · UniProt Q5SIH3
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