MolNFT v1 · #98952 · protein + DNA
Crystal structure of the I-smami laglidadg homing endonuclease bound to cleaved DNA
4LOX · Laglidadg homing endonuclease I-smami: “Crystal structure of the I-smami laglidadg homing endonuclease bound to cleaved DNA”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.70). MolNFT v1 #98952 on GenesisL1: 3D…
- PDB
- 4LOX
- Type
- protein + DNA
- Length
- 350 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laglidadg homing endonuclease I-smami; DNA (5'-D(*CP*GP*TP*AP*CP*AP*CP*CP*TP*GP*AP*TP*AP*A…
- UniProt
- F7WD42
- Ligands
- MG
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Laglidadg homing endonuclease I-smami | protein | 300 | 49% helix, 22% strand | F7WD42 |
| B | DNA (5'-D(*CP*GP*TP*AP*CP*AP*CP*CP*TP*GP*AP*TP*AP*A)-3') | dna | 14 | — | — |
| C | DNA (5'-D(P*TP*GP*GP*AP*GP*GP*AP*TP*AP*CP*C)-3') | dna | 11 | — | — |
| D | DNA (5'-D(*GP*GP*TP*AP*TP*CP*CP*TP*CP*CP*AP*TP*TP*AP*T)- 3') | dna | 15 | — | — |
| E | DNA (5'-D(P*CP*AP*GP*GP*TP*GP*TP*AP*CP*G)-3') | dna | 10 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C, D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.70 | 0.96 | 25 | empty |
| 2 | 207 | 0.65 | 0.85 | 28 | empty |
| 3 | 187 | 0.51 | 0.79 | 27 | empty |
| 4 | 79 | 0.38 | 0.78 | 16 | empty |
| 5 | 67 | 0.38 | 0.79 | 22 | empty |
Interfaces
10 interfaces between chains.
- A–D · 1020 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–B · 925 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–E · 631 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–C · 619 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–D · 581 Ų buried · 46 hydrogen bonds · nucleic-nucleic
Compared structures
- 4LOX · Crystal structure of the I-SmaMI LAGLIDADG homing endonuclease bound to cleaved 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 F7WD42
- Elsewhere: RCSB PDB 4LOX · PDBe 4LOX · UniProt F7WD42
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