MolNFT v1 · #136684 · protein + DNA
Original engineered variant of I-onui meganuclease targeting the HIV integrase gene; harbors 49 point mutations relative to wild-type I- onui
5V0Q · I-ONUI_E-VHIVINT_V1: “Original engineered variant of I-onui meganuclease targeting the HIV integrase gene; harbors 49 point…”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.67). MolNFT v1 #136684 on GenesisL1: 3D…
- PDB
- 5V0Q
- Type
- protein + DNA
- Length
- 343 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- I-ONUI_E-VHIVINT_V1; DNA (26-mer)
- Ligands
- CA
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | I-ONUI_E-VHIVINT_V1 | protein | 291 | 51% helix, 23% strand | — |
| B | DNA (26-mer) | dna | 26 | — | — |
| C | DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.67 | 0.86 | 28 | CA |
| 2 | 282 | 0.59 | 0.79 | 31 | empty |
| 3 | 121 | 0.45 | 0.78 | 17 | empty |
| 4 | 87 | 0.35 | 0.75 | 15 | empty |
| 5 | 63 | 0.32 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1674 Ų buried · 34 hydrogen bonds · protein-nucleic
- A–B · 1607 Ų buried · 37 hydrogen bonds · protein-nucleic
- B–C · 1249 Ų buried · 95 hydrogen bonds · nucleic-nucleic
Compared structures
- 5V0Q · Original engineered variant of I-OnuI meganuclease targeting the HIV integrase gene… · 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 5V0Q · PDBe 5V0Q
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