MolNFT v1 · #148832 · protein
Structure of the human line-1 ORF1P coiled coil domain
6FIA · Line-1 retrotransposable element ORF1 protein: “Structure of the human line-1 ORF1P coiled coil domain”. X-ray diffraction, 1 ligand (CL), 7 pockets (best druggability 0.64). MolNFT v1 #148832 on GenesisL1: 3D structure, binding…
- PDB
- 6FIA
- Type
- protein
- Length
- 572 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Line-1 retrotransposable element ORF1 protein
- UniProt
- Q9UN81
- Ligands
- CL
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 94% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Line-1 retrotransposable element ORF1 protein | protein | 103 | 97% helix, 0% strand | Q9UN81 |
| B | Line-1 retrotransposable element ORF1 protein | protein | 100 | 97% helix, 0% strand | Q9UN81 |
| C | Line-1 retrotransposable element ORF1 protein | protein | 89 | 94% helix, 0% strand | Q9UN81 |
| D | Line-1 retrotransposable element ORF1 protein | protein | 104 | 88% helix, 0% strand | Q9UN81 |
| E, F | Line-1 retrotransposable element ORF1 protein | protein | 88 | 95% helix, 0% strand | Q9UN81 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 456 | 0.64 | 0.77 | 48 | empty |
| 2 | 403 | 0.62 | 0.77 | 49 | empty |
| 3 | 185 | 0.48 | 0.76 | 22 | empty |
| 4 | 83 | 0.36 | 0.76 | 16 | empty |
| 5 | 61 | 0.36 | 0.78 | 18 | CL |
Interfaces
10 interfaces between chains.
- A–B · 2207 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1995 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1914 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1900 Ų buried · 25 hydrogen bonds · protein-protein
- D–F · 1850 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6FIA · Structure of the human LINE-1 ORF1p coiled coil domain · the same entry in another collection · chain F against F, TM-score 1.00
- Q9UN81 · AlphaFold monomer V2.0 prediction for line-1 retrotransposable element ORF1 protein… · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q9UN81
- Elsewhere: RCSB PDB 6FIA · PDBe 6FIA · UniProt Q9UN81
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