Research workbench
Coevolution of a homing endonuclease and its host target sequence
Analyse Coevolution of a homing endonuclease and its host target sequence in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QOJ
- Type
- protein + DNA
- Length
- 313 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laglidadg endonuclease; I-anii DNA target SEQ1; I-anii DNA target SEQ2
- UniProt
- H9D0N7
- Ligands
- MG
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Z | Laglidadg endonuclease | protein | 254 | 44% helix, 20% strand | H9D0N7 |
| X | I-anii DNA target SEQ1 | dna | 29 | — | — |
| Y | I-anii DNA target SEQ2 | dna | 30 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains Z, X, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.48 | 0.82 | 23 | empty |
| 2 | 142 | 0.43 | 0.76 | 24 | empty |
| 3 | 67 | 0.39 | 0.80 | 18 | empty |
| 4 | 59 | 0.27 | 0.73 | 11 | empty |
Interfaces
3 interfaces between chains.
- Z–Y · 1486 Ų buried · 19 hydrogen bonds · protein-nucleic
- Z–X · 1451 Ų buried · 36 hydrogen bonds · protein-nucleic
- X–Y · 1419 Ų buried · 126 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 2QOJ · Coevolution of a homing endonuclease and its host target sequence · the same entry in another collection · chain Z against Z, 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
- Every structure of UniProt H9D0N7
- Elsewhere: RCSB PDB 2QOJ · PDBe 2QOJ · UniProt H9D0N7
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