Research workbench
Crystal structure of laglidadg meganuclease I-aabmi bound to uncleaved DNA
Analyse Crystal structure of laglidadg meganuclease I-aabmi bound to uncleaved DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YIT
- Type
- protein + DNA
- Length
- 647 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Meganuclease I-aabmi; DNA (25-mer); DNA (25MER)
- Ligands
- CA
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Meganuclease I-aabmi | protein | 272 | 47% helix, 21% strand | — |
| D | Meganuclease I-aabmi | protein | 277 | 49% helix, 20% strand | — |
| B | DNA (25-mer) | dna | 25 | — | — |
| C | DNA (25-mer) | dna | 25 | — | — |
| E | DNA (25MER) | dna | 24 | — | — |
| F | DNA (25-mer) | dna | 24 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.73 | 0.93 | 28 | empty |
| 2 | 107 | 0.61 | 0.88 | 23 | empty |
| 3 | 231 | 0.59 | 0.81 | 27 | empty |
| 4 | 420 | 0.59 | 0.75 | 34 | empty |
| 5 | 91 | 0.58 | 0.87 | 20 | empty |
Interfaces
7 interfaces between chains.
- A–C · 1525 Ų buried · 32 hydrogen bonds · protein-nucleic
- D–F · 1500 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–B · 1311 Ų buried · 31 hydrogen bonds · protein-nucleic
- D–E · 1288 Ų buried · 27 hydrogen bonds · protein-nucleic
- B–C · 1272 Ų buried · 111 hydrogen bonds · nucleic-nucleic
Compared structures
- 4YIT · Crystal Structure of LAGLIDADG Meganuclease I-AabMI Bound to Uncleaved 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
- Elsewhere: RCSB PDB 4YIT · PDBe 4YIT
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