MolNFT v1 · #25542 · protein
Endonuclease domain of human LINE1 ORF2P
1VYB · ORF2 contains a reverse transcriptase domain: “Endonuclease domain of human LINE1 ORF2P”. X-ray diffraction, 2 ligands (SO4, SO3), 4 pockets (best druggability 0.75). MolNFT v1 #25542 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1VYB
- Type
- protein
- Length
- 469 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORF2 contains a reverse transcriptase domain
- UniProt
- Q15606
- Ligands
- SO4, SO3
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ORF2 contains a reverse transcriptase domain | protein | 236 | 23% helix, 34% strand | Q15606 |
| B | ORF2 contains a reverse transcriptase domain | protein | 233 | 23% helix, 36% strand | Q15606 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- SO3 · Sulfite ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.75 | 0.78 | 89 | SO4, SO3 |
| 2 | 63 | 0.48 | 0.84 | 12 | empty |
| 3 | 103 | 0.34 | 0.73 | 28 | empty |
| 4 | 61 | 0.26 | 0.72 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 445 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1VYB · Endonuclease domain of human LINE1 ORF2p · 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 Q15606
- Elsewhere: RCSB PDB 1VYB · PDBe 1VYB · UniProt Q15606
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