Research workbench
Crystal structure of an extended tRNA anticodon stem loop in complex with its cognate mRNA cggg in the context of the thermus thermophilus 30S subunit.
Analyse Crystal structure of an extended tRNA anticodon stem loop in complex with its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2UXD
- Type
- protein + RNA
- Length
- 3,892 residues
- Chains
- 23
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 23 distinct chains · 31% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S ribosomal RNA | rna | 1484 | — | — |
| B | Ribosomal protein S2 | protein | 234 | 37% helix, 9% strand | P80371 |
| C | Ribosomal protein S3 | protein | 206 | 26% helix, 12% strand | P80372 |
| D | Ribosomal protein S4 | protein | 208 | 37% helix, 6% strand | P80373 |
| E | Ribosomal protein S5 | protein | 150 | 29% helix, 36% strand | Q5SHQ5 |
| F | Ribosomal protein S6 | protein | 101 | 30% helix, 28% strand | Q5SLP8 |
| G | Ribosomal protein S7 | protein | 155 | 40% helix, 3% strand | P17291 |
| H | Ribosomal protein S8 | protein | 138 | 27% helix, 29% strand | Q5SHQ2 |
| I | Ribosomal protein S9 | protein | 127 | 20% helix, 15% strand | P80374 |
| J | Ribosomal protein S10 | protein | 98 | 0% helix, 17% strand | Q5SHN7 |
| K | Ribosomal protein S11 | protein | 119 | 28% helix, 29% strand | P80376 |
| L | Ribosomal protein S12 | protein | 124 | 5% helix, 14% strand | Q5SHN3 |
| M | Ribosomal protein S13 | protein | 125 | 49% helix, 2% strand | P80377 |
| N | Ribosomal protein S14 | protein | 60 | 30% helix, 2% strand | Q5SHQ1 |
| O | Ribosomal protein S15 | protein | 88 | 70% helix, 0% strand | Q5SJ76 |
| P | Ribosomal protein S16 | protein | 83 | 19% helix, 25% strand | Q5SJH3 |
| Q | Ribosomal protein S17 | protein | 104 | 13% helix, 52% strand | Q5SHP7 |
| R | Ribosomal protein S18 | protein | 73 | 36% helix, 7% strand | Q5SLQ0 |
| S | Ribosomal protein S19 | protein | 80 | 16% helix, 16% strand | Q5SHP2 |
| T | Ribosomal protein S20 | protein | 99 | 68% helix, 0% strand | P80380 |
| V | Ribosomal protein thx | protein | 24 | 25% helix, 8% strand | Q5SIH3 |
| X | Anticodon stem-loop of transfer RNA with anticodon cccg | rna | 4 | — | — |
| Y | A-site messenger RNA fragment cggg | rna | 8 | — | — |
Ligands and binding sites
- PAR · Paromomycin · ligand · chains A
- MG · Magnesium ion · metal · 70 copies · chains A, C, V, L, J, E
- K · Potassium ion · metal · 8 copies · chains A
- 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 | 1075 | 0.89 | 0.91 | 89 | MG |
| 2 | 989 | 0.85 | 0.87 | 80 | MG |
| 3 | 893 | 0.85 | 0.88 | 73 | MG |
| 4 | 709 | 0.85 | 0.89 | 70 | MG |
| 5 | 767 | 0.84 | 0.88 | 70 | empty |
Interfaces
48 interfaces between chains.
- A–L · 3315 Ų buried · 93 hydrogen bonds · protein-nucleic
- A–D · 3151 Ų buried · 84 hydrogen bonds · protein-nucleic
- A–I · 3054 Ų buried · 90 hydrogen bonds · protein-nucleic
- A–Q · 2737 Ų buried · 56 hydrogen bonds · protein-nucleic
- A–T · 2421 Ų buried · 64 hydrogen bonds · protein-nucleic
Compared structures
- 2UXD · Crystal structure of an extended tRNA anticodon stem loop in complex with its cognate… · the same entry in another collection · chain A against A, 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 2UXD · PDBe 2UXD · 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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