Research workbench
The homing endonuclease I-wcai bound to its DNA recognition sequence
Analyse The homing endonuclease I-wcai bound to its DNA recognition sequence in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X1J
- Type
- protein + DNA
- Length
- 275 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable intron-encoded endonuclease 1; DNA (25-mer)
- EC
- 3.1.-.-
- UniProt
- Q34807
- Ligands
- K
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable intron-encoded endonuclease 1 (EC 3.1.-.-) | protein | 226 | 42% helix, 19% strand | Q34807 |
| C | DNA (25-mer) | dna | 24 | — | — |
| D | DNA (25-mer) | dna | 25 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, C, D
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 | 53 | 0.59 | 0.92 | 18 | empty |
| 2 | 198 | 0.55 | 0.79 | 24 | K |
| 3 | 126 | 0.48 | 0.80 | 22 | K |
| 4 | 59 | 0.32 | 0.76 | 10 | empty |
| 5 | 67 | 0.31 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1345 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–D · 1226 Ų buried · 22 hydrogen bonds · protein-nucleic
- C–D · 1177 Ų buried · 99 hydrogen bonds · nucleic-nucleic
Compared structures
- 6X1J · The homing endonuclease I-WcaI bound to its DNA recognition sequence · the same entry in another collection · chain A against A, TM-score 1.00
- Q34807 · AlphaFold monomer V2.0 prediction for probable intron-encoded endonuclease 1 (Q34807) · 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 Q34807
- Elsewhere: RCSB PDB 6X1J · PDBe 6X1J · UniProt Q34807
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