Research workbench
H98Q mutant of the homing endonuclease I-ppoi complexed with DNA
Analyse H98Q mutant of the homing endonuclease I-ppoi complexed with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O6M
- Type
- protein + DNA
- Length
- 366 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*DTP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DAP*D…
- EC
- 3.1.-.-
- UniProt
- Q94702
- Ligands
- ZN, MG
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 5'-D(*DTP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DAP*D GP*DAP*DGP*DAP*DGP*DTP*DCP*DA)-3' | dna | 21 | — | — |
| A, B | Intron-encoded endonuclease I-ppoi (EC 3.1.-.-) | protein | 162 | 19% helix, 31% strand | Q94702 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains C, B, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.62 | 0.88 | 24 | empty |
| 2 | 182 | 0.48 | 0.76 | 26 | empty |
| 3 | 171 | 0.47 | 0.76 | 27 | empty |
| 4 | 130 | 0.41 | 0.75 | 25 | MG |
| 5 | 72 | 0.33 | 0.75 | 13 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2542 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 917 Ų buried · 72 hydrogen bonds · nucleic-nucleic
- C–A · 617 Ų buried · 5 hydrogen bonds · protein-nucleic
- D–B · 600 Ų buried · 4 hydrogen bonds · protein-nucleic
- D–A · 582 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 2O6M · H98Q mutant of the homing endonuclease I-PPOI complexed with DNA · the same entry in another collection · chain C against C, TM-score 1.00
- Q94702 · AlphaFold monomer V2.0 prediction for intron-encoded endonuclease I-ppoi (Q94702) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q94702
- Elsewhere: RCSB PDB 2O6M · PDBe 2O6M · UniProt Q94702
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