Research workbench
Crystal structure of a line-1 type transposase domain-containing protein 1 (L1TD1) from homo sapiens at 2.73 a resolution
Analyse Crystal structure of a line-1 type transposase domain-containing protein 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SOO
- Type
- protein
- Length
- 260 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Line-1 type transposase domain-containing protein 1
- UniProt
- Q5T7N2
- Ligands
- SO4, CL
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Line-1 type transposase domain-containing protein 1 | protein | 87 | 29% helix, 14% strand | Q5T7N2 |
| C | Line-1 type transposase domain-containing protein 1 | protein | 86 | 28% helix, 26% strand | Q5T7N2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.69 | 0.78 | 57 | SO4 |
| 2 | 132 | 0.45 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2579 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 708 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 379 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (methylation, engineered).
Compared structures
- 3SOO · Crystal structure of a LINE-1 type transposase domain-containing protein 1 (L1TD1) from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5T7N2 · AlphaFold monomer V2.0 prediction for line-1 type transposase domain- containing protein… · a predicted model of the same protein · chain A against A, TM-score 0.54
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 Q5T7N2
- Elsewhere: RCSB PDB 3SOO · PDBe 3SOO · UniProt Q5T7N2
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