MolNFT v1 · #134578 · protein + DNA
Engineered variant of I-onui meganuclease targeting the HIV integrase gene; harbors 47 point mutations relative to wild-type I-onui
5T8D · I-ONUI_E-VHIVINT_V2: “Engineered variant of I-onui meganuclease targeting the HIV integrase gene; harbors 47 point mutations…”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.67). MolNFT v1 #134578 on GenesisL1: 3D…
- PDB
- 5T8D
- Type
- protein + DNA
- Length
- 344 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- I-ONUI_E-VHIVINT_V2; DNA (26-mer)
- Ligands
- CA
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | I-ONUI_E-VHIVINT_V2 | protein | 292 | 51% helix, 21% strand | — |
| B | DNA (26-mer) | dna | 26 | — | — |
| C | DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.67 | 0.90 | 18 | empty |
| 2 | 243 | 0.61 | 0.81 | 34 | empty |
| 3 | 126 | 0.51 | 0.81 | 26 | empty |
| 4 | 52 | 0.31 | 0.77 | 12 | empty |
| 5 | 65 | 0.31 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1742 Ų buried · 36 hydrogen bonds · protein-nucleic
- A–B · 1602 Ų buried · 31 hydrogen bonds · protein-nucleic
- B–C · 1256 Ų buried · 103 hydrogen bonds · nucleic-nucleic
Compared structures
- 5T8D · Engineered variant of I-OnuI meganuclease targeting the HIV integrase gene; harbors 47… · 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
- Elsewhere: RCSB PDB 5T8D · PDBe 5T8D
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