Research workbench
Structure of the human line-1 ORF1P trimer
Analyse Structure of the human line-1 ORF1P trimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YKO
- Type
- protein
- Length
- 598 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Line-1 ORF1P
- UniProt
- Q15605
- Ligands
- CL
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Line-1 ORF1P | protein | 204 | 50% helix, 19% strand | Q15605 |
| B | Line-1 ORF1P | protein | 193 | 52% helix, 21% strand | Q15605 |
| C | Line-1 ORF1P | protein | 201 | 54% helix, 19% strand | Q15605 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.75 | 0.81 | 81 | empty |
| 2 | 849 | 0.69 | 0.75 | 86 | empty |
| 3 | 508 | 0.64 | 0.76 | 48 | empty |
| 4 | 108 | 0.39 | 0.76 | 21 | empty |
| 5 | 74 | 0.32 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1299 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1269 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1223 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2YKO · Structure of the human LINE-1 ORF1p trimer · 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 Q15605
- Elsewhere: RCSB PDB 2YKO · PDBe 2YKO · UniProt Q15605
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