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
- 2YKQ
- 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, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Line-1 ORF1P | protein | 200 | 52% helix, 18% strand | Q15605 |
| B | Line-1 ORF1P | protein | 198 | 51% helix, 17% strand | Q15605 |
| C | Line-1 ORF1P | protein | 200 | 53% helix, 20% 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 593 | 0.75 | 0.82 | 74 | empty |
| 2 | 305 | 0.56 | 0.76 | 35 | empty |
| 3 | 216 | 0.53 | 0.77 | 24 | empty |
| 4 | 237 | 0.50 | 0.75 | 24 | empty |
| 5 | 202 | 0.49 | 0.76 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1308 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1231 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1160 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2YKQ · 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 2YKQ · PDBe 2YKQ · UniProt Q15605
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