MolNFT v1 · #182932 · protein + DNA
Line-1 endonuclease domain complex with DNA
7N94 · Line-1 retrotransposable element ORF2 protein: “Line-1 endonuclease domain complex with DNA”. X-ray diffraction, 10 pockets (best druggability 0.71). MolNFT v1 #182932 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7N94
- Type
- protein + DNA
- Length
- 534 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Line-1 retrotransposable element ORF2 protein; DNA (5'…
- EC
- 2.7.7.49, 3.1.21.-
- UniProt
- O00370
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Line-1 retrotransposable element ORF2 protein (EC 2.7.7.49, 3.1.21.-) | protein | 232 | 25% helix, 34% strand | O00370 |
| D | DNA (5'- D(*GP*CP*TP*CP*CP*TP*TP*TP*TP*TP*AP*AP*GP*GP*GP*CP*TP*A)-3') | dna | 18 | — | — |
| E | DNA (5'- D(*AP*GP*CP*CP*CP*TP*TP*AP*AP*AP*AP*AP*GP*GP*AP*GP*CP*T)-3') | dna | 17 | — | — |
| F | DNA (5'- D(*GP*CP*TP*CP*CP*TP*TP*TP*TP*TP*AP*AP*GP*GP*GP*CP*TP*A)-3') | dna | 17 | — | — |
| G | DNA (5'- D(*AP*GP*CP*CP*CP*TP*TP*AP*AP*AP*AP*AP*GP*GP*AP*GP*CP*T)-3') | dna | 18 | — | — |
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.71 | 0.81 | 40 | empty |
| 2 | 586 | 0.69 | 0.78 | 55 | empty |
| 3 | 506 | 0.65 | 0.78 | 40 | empty |
| 4 | 462 | 0.65 | 0.78 | 39 | empty |
| 5 | 176 | 0.65 | 0.86 | 24 | empty |
Interfaces
11 interfaces between chains.
- F–G · 763 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- D–E · 759 Ų buried · 67 hydrogen bonds · nucleic-nucleic
- A–D · 534 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–F · 523 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–G · 378 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
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 O00370
- Elsewhere: RCSB PDB 7N94 · PDBe 7N94 · UniProt O00370
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