Research workbench
Engineered variant of I-onui meganuclease targeting the anopheles AGAP007280 gene; harbors 38 point mutations relative to wild-type I- onui
Analyse Engineered variant of I-onui meganuclease targeting the anopheles AGAP007280… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T2N
- Type
- protein + DNA
- Length
- 343 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- I-ONUI_E-AG007820; DNA (26-mer)
- Ligands
- CA
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | I-ONUI_E-AG007820 | protein | 291 | 50% helix, 23% strand | — |
| B | DNA (26-mer) | dna | 26 | — | — |
| C | DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.69 | 0.89 | 26 | CA |
| 2 | 56 | 0.65 | 0.95 | 22 | empty |
| 3 | 89 | 0.51 | 0.85 | 19 | CA |
| 4 | 95 | 0.41 | 0.78 | 17 | empty |
| 5 | 55 | 0.29 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1697 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–C · 1647 Ų buried · 35 hydrogen bonds · protein-nucleic
- B–C · 1260 Ų buried · 109 hydrogen bonds · nucleic-nucleic
Compared structures
- 5T2N · Engineered variant of I-OnuI meganuclease targeting the Anopheles AGAP007280 gene… · the same entry in another collection · chain B against B, 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 5T2N · PDBe 5T2N
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