MolNFT v1 · #134388 · protein + DNA
Engineered variant of I-onui meganuclease targeting the anopheles AGAP011377 gene; harbors 53 point mutations relative to wild-type I- onui
5T2O · I-ONUI_E-AG011377: “Engineered variant of I-onui meganuclease targeting the anopheles AGAP011377 gene; harbors 53 point mutations…”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.59). MolNFT v1 #134388 on…
- PDB
- 5T2O
- Type
- protein + DNA
- Length
- 345 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- I-ONUI_E-AG011377; DNA (26-mer)
- Ligands
- CA
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | I-ONUI_E-AG011377 | protein | 293 | 48% helix, 22% 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.59 | 0.83 | 26 | empty |
| 2 | 136 | 0.52 | 0.81 | 20 | empty |
| 3 | 138 | 0.44 | 0.77 | 22 | empty |
| 4 | 71 | 0.44 | 0.82 | 22 | CA |
| 5 | 68 | 0.35 | 0.77 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1636 Ų buried · 33 hydrogen bonds · protein-nucleic
- A–C · 1613 Ų buried · 30 hydrogen bonds · protein-nucleic
- B–C · 1264 Ų buried · 101 hydrogen bonds · nucleic-nucleic
Compared structures
- 5T2O · Engineered variant of I-OnuI meganuclease targeting the Anopheles AGAP011377 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 5T2O · PDBe 5T2O
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