Research workbench
Crystal structure of the I-ltrwi laglidadg homing endonuclease bound to target DNA.
Analyse Crystal structure of the I-ltrwi laglidadg homing endonuclease bound to target… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LQ0
- Type
- protein + DNA
- Length
- 350 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laglidadg homing endonuclease; Top strand DNA target; Bottom strand DNA target
- UniProt
- E0YCK3
- Ligands
- CA
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Laglidadg homing endonuclease | protein | 298 | 50% helix, 20% strand | E0YCK3 |
| B | Top strand DNA target | dna | 26 | — | — |
| C | Bottom strand DNA target | dna | 26 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.69 | 0.87 | 25 | empty |
| 2 | 176 | 0.55 | 0.81 | 23 | empty |
| 3 | 119 | 0.44 | 0.77 | 18 | empty |
| 4 | 114 | 0.40 | 0.76 | 21 | empty |
| 5 | 54 | 0.33 | 0.78 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1583 Ų buried · 33 hydrogen bonds · protein-nucleic
- A–C · 1543 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–C · 1250 Ų buried · 109 hydrogen bonds · nucleic-nucleic
Compared structures
- 4LQ0 · Crystal structure of the I-LtrWI LAGLIDADG homing endonuclease bound to target DNA. · 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
- Every structure of UniProt E0YCK3
- Elsewhere: RCSB PDB 4LQ0 · PDBe 4LQ0 · UniProt E0YCK3
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