Research workbench
Crystal structure of MNM5U34T6A37-trnalysuuu complexed with aag-mRNA in the decoding center
Analyse Crystal structure of MNM5U34T6A37-trnalysuuu complexed with aag-mRNA in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XMO
- Type
- protein + RNA
- Length
- 3,917 residues
- Chains
- 23
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S ribosomal RNA; A-site messenger RNA; Anticodon transfer RNA; 30S ribosomal protein…
- UniProt
- P80371, P80372, P80373, P27152, P23370, P17291, P62668, P80374, P80375, P80376, P80377, P24320, P80378, P80379, P62658, P80382, P80381, P80380, P62612
- Ligands
- PAR, MG, ZN
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 23 distinct chains · 33% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S ribosomal RNA | rna | 1507 | — | — |
| W | A-site messenger RNA | rna | 3 | — | — |
| X | Anticodon transfer RNA | rna | 11 | — | — |
| B | 30S ribosomal protein S2 | protein | 234 | 38% helix, 9% strand | P80371 |
| C | 30S ribosomal protein S3 | protein | 206 | 31% helix, 12% strand | P80372 |
| D | 30S ribosomal protein S4 | protein | 208 | 38% helix, 8% strand | P80373 |
| E | 30S ribosomal protein S5 | protein | 150 | 30% helix, 38% strand | P27152 |
| F | 30S ribosomal protein S6 | protein | 101 | 26% helix, 31% strand | P23370 |
| G | 30S ribosomal protein S7 | protein | 155 | 53% helix, 6% strand | P17291 |
| H | 30S ribosomal protein S8 | protein | 138 | 28% helix, 27% strand | P62668 |
| I | 30S ribosomal protein S9 | protein | 127 | 30% helix, 19% strand | P80374 |
| J | 30S ribosomal protein S10 | protein | 98 | 7% helix, 27% strand | P80375 |
| K | 30S ribosomal protein S11 | protein | 119 | 24% helix, 29% strand | P80376 |
| L | 30S ribosomal protein S12 | protein | 124 | 7% helix, 22% strand | — |
| M | 30S ribosomal protein S13 | protein | 125 | 49% helix, 2% strand | P80377 |
| N | 30S ribosomal protein S14 | protein | 60 | 17% helix, 2% strand | P24320 |
| O | 30S ribosomal protein S15 | protein | 88 | 75% helix, 0% strand | P80378 |
| P | 30S ribosomal protein S16 | protein | 83 | 20% helix, 29% strand | P80379 |
| Q | 30S ribosomal protein S17 | protein | 104 | 12% helix, 46% strand | P62658 |
| R | 30S ribosomal protein S18 | protein | 73 | 38% helix, 7% strand | P80382 |
| S | 30S ribosomal protein S19 | protein | 80 | 13% helix, 15% strand | P80381 |
| T | 30S ribosomal protein S20 | protein | 99 | 69% helix, 0% strand | P80380 |
| V | 30S ribosomal protein thx | protein | 24 | 25% helix, 8% strand | P62612 |
Ligands and binding sites
- PAR · Paromomycin · ligand · chains A
- MG · Magnesium ion · metal · 107 copies · chains A, N, T, L, W, J, P, X
- 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 | 1030 | 0.89 | 0.91 | 84 | MG |
| 2 | 981 | 0.86 | 0.88 | 85 | MG |
| 3 | 708 | 0.85 | 0.89 | 68 | MG |
| 4 | 1073 | 0.85 | 0.86 | 84 | MG |
| 5 | 749 | 0.84 | 0.88 | 77 | empty |
Interfaces
48 interfaces between chains.
- A–L · 3328 Ų buried · 89 hydrogen bonds · protein-nucleic
- A–I · 3010 Ų buried · 107 hydrogen bonds · protein-nucleic
- A–Q · 2701 Ų buried · 77 hydrogen bonds · protein-nucleic
- A–T · 2697 Ų buried · 71 hydrogen bonds · protein-nucleic
- A–D · 2531 Ų buried · 78 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1XMO · Crystal Structure of mnm5U34t6A37-tRNALysUUU Complexed with AAG-mRNA in the Decoding… · the same entry in another collection · chain I against I, 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 P27152
- Every structure of UniProt P23370
- Every structure of UniProt P17291
- Every structure of UniProt P62668
- Every structure of UniProt P80374
- Every structure of UniProt P80375
- Every structure of UniProt P80376
- Every structure of UniProt P80377
- Every structure of UniProt P24320
- Every structure of UniProt P80378
- Every structure of UniProt P80379
- Every structure of UniProt P62658
- Every structure of UniProt P80382
- Every structure of UniProt P80381
- Every structure of UniProt P80380
- Every structure of UniProt P62612
- Elsewhere: RCSB PDB 1XMO · PDBe 1XMO · UniProt P80371 · UniProt P80372 · UniProt P80373 · UniProt P27152 · UniProt P23370 · UniProt P17291 · UniProt P62668 · UniProt P80374 · UniProt P80375 · UniProt P80376 · UniProt P80377 · UniProt P24320 · UniProt P80378 · UniProt P80379 · UniProt P62658 · UniProt P80382 · UniProt P80381 · UniProt P80380 · UniProt P62612
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