Research workbench
Structure of human transfer RNA visualized in the cytomegalovirus, a DNA virus
Analyse Structure of human transfer RNA visualized in the cytomegalovirus, a DNA virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LJ3
- Type
- protein + RNA
- Length
- 2,789 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tegument protein PP150; RNA (75-mer)
- UniProt
- P08318
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 63% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| z | Tegument protein PP150 | protein | 284 | 63% helix, 0% strand | P08318 |
| 0, y, 5, 6, 4, 8, 9, 7 | Tegument protein PP150 | protein | 285 | 63% helix, 0% strand | P08318 |
| A, B, C | RNA (75-mer) | rna | 75 | — | — |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.81 | 0.83 | 61 | empty |
| 2 | 1100 | 0.80 | 0.82 | 58 | empty |
| 3 | 1061 | 0.79 | 0.81 | 56 | empty |
| 4 | 945 | 0.77 | 0.80 | 79 | empty |
| 5 | 896 | 0.76 | 0.80 | 69 | empty |
Interfaces
15 interfaces between chains.
- 8–9 · 818 Ų buried · 9 hydrogen bonds · protein-protein
- z–0 · 775 Ų buried · 7 hydrogen bonds · protein-protein
- 5–6 · 705 Ų buried · 10 hydrogen bonds · protein-protein
- z–A · 543 Ų buried · 10 hydrogen bonds · protein-nucleic
- 8–C · 521 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 7LJ3 · Structure of human transfer RNA visualized in the cytomegalovirus, a DNA virus · the same entry in another collection · chain z against z, 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 P08318
- Elsewhere: RCSB PDB 7LJ3 · PDBe 7LJ3 · UniProt P08318
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