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
- 7LIV
- Type
- protein
- Length
- 5,903 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein; Tegument protein PP150; Small capsomere-interacting protein…
- UniProt
- P16729, P08318, Q7M6N6, P16783, P16728
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 7 distinct chains · 37% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| J, C | Major capsid protein | protein | 1348 | 34% helix, 14% strand | P16729 |
| A | Major capsid protein | protein | 1328 | 35% helix, 14% strand | P16729 |
| 5, 6, 4 | Tegument protein PP150 | protein | 285 | 66% helix, 0% strand | P08318 |
| Z, D, E | Small capsomere-interacting protein | protein | 63 | 60% helix, 0% strand | Q7M6N6 |
| p | Triplex capsid protein 1 | protein | 290 | 26% helix, 30% strand | P16783 |
| q | Triplex capsid protein 2 | protein | 241 | 37% helix, 15% strand | P16728 |
| r | Triplex capsid protein 2 | protein | 304 | 34% helix, 16% strand | P16728 |
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 | 1105 | 0.83 | 0.84 | 92 | empty |
| 2 | 770 | 0.81 | 0.84 | 74 | empty |
| 3 | 690 | 0.81 | 0.85 | 63 | empty |
| 4 | 730 | 0.81 | 0.84 | 64 | empty |
| 5 | 1064 | 0.80 | 0.82 | 98 | empty |
Interfaces
35 interfaces between chains.
- J–C · 2460 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 2448 Ų buried · 17 hydrogen bonds · protein-protein
- q–r · 2429 Ų buried · 15 hydrogen bonds · protein-protein
- J–A · 2355 Ų buried · 18 hydrogen bonds · protein-protein
- A–p · 1576 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7LIV · Structure of human transfer RNA visualized in the cytomegalovirus, a DNA virus · 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 P16729
- Every structure of UniProt P08318
- Every structure of UniProt Q7M6N6
- Every structure of UniProt P16783
- Every structure of UniProt P16728
- Elsewhere: RCSB PDB 7LIV · PDBe 7LIV · UniProt P16729 · UniProt P08318 · UniProt Q7M6N6 · UniProt P16783 · UniProt P16728
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