Research workbench
Laglidadg homing endonuclease I-crei / DNA product complex with magnesium
Analyse Laglidadg homing endonuclease I-crei / DNA product complex with magnesium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G9Z
- Type
- protein + DNA
- Length
- 352 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*A)- 3'…
- EC
- 3.1.-.-
- UniProt
- P05725
- Ligands
- MG
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 54% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*A)- 3' | dna | 14 | — | — |
| D | 5'-D(P*GP*AP*CP*AP*GP*TP*TP*TP*CP*G)-3' | dna | 10 | — | — |
| E | 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*C)- 3' | dna | 14 | — | — |
| F | 5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*GP*C)-3' | dna | 10 | — | — |
| A, B | DNA endonuclease I-crei (EC 3.1.-.-) | protein | 152 | 54% helix, 21% strand | P05725 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains C, D, E, F, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.71 | 0.94 | 29 | empty |
| 2 | 109 | 0.69 | 0.92 | 27 | empty |
Interfaces
15 interfaces between chains.
- A–B · 1003 Ų buried · 16 hydrogen bonds · protein-protein
- C–B · 874 Ų buried · 17 hydrogen bonds · protein-nucleic
- E–A · 861 Ų buried · 13 hydrogen bonds · protein-nucleic
- F–B · 805 Ų buried · 22 hydrogen bonds · protein-nucleic
- D–A · 787 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 1G9Z · Laglidadg homing endonuclease I-crei / DNA product complex with magnesium · the same entry in another collection · chain B against B, TM-score 1.00
- P05725 · AlphaFold monomer V2.0 prediction for DNA endonuclease I-crei (P05725) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P05725
- Elsewhere: RCSB PDB 1G9Z · PDBe 1G9Z · UniProt P05725
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