Research workbench
Crystal structure of laglidadg homing endonuclease I-gzeii in complex with DNA target
Analyse Crystal structure of laglidadg homing endonuclease I-gzeii in complex with DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z1X
- Type
- protein + DNA
- Length
- 688 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (27-mer); Laglidadg endonuclease
- UniProt
- A5J036
- Ligands
- CA
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | DNA (27-mer) | dna | 27 | — | — |
| D, F | DNA (27-mer) | dna | 26 | — | — |
| A, B | Laglidadg endonuclease | protein | 291 | 49% helix, 20% strand | A5J036 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains E, F, A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.74 | 0.79 | 68 | empty |
| 2 | 169 | 0.61 | 0.84 | 21 | empty |
| 3 | 143 | 0.58 | 0.83 | 24 | empty |
| 4 | 307 | 0.56 | 0.77 | 33 | empty |
| 5 | 133 | 0.53 | 0.82 | 29 | empty |
Interfaces
10 interfaces between chains.
- F–A · 1400 Ų buried · 28 hydrogen bonds · protein-nucleic
- D–B · 1392 Ų buried · 26 hydrogen bonds · protein-nucleic
- C–B · 1349 Ų buried · 31 hydrogen bonds · protein-nucleic
- E–A · 1324 Ų buried · 26 hydrogen bonds · protein-nucleic
- C–D · 1306 Ų buried · 100 hydrogen bonds · nucleic-nucleic
Compared structures
- 4Z1X · Crystal structure of LAGLIDADG homing endonuclease I-GzeII in complex with DNA target · 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 A5J036
- Elsewhere: RCSB PDB 4Z1X · PDBe 4Z1X · UniProt A5J036
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