MolNFT v1 · #90311 · protein + DNA
Crystal structure of I-gzeii laglidadg homing endonuclease in complex with DNA target site
4EFJ · DNA target site top strand: “Crystal structure of I-gzeii laglidadg homing endonuclease in complex with DNA target site”. X-ray diffraction, 1 ligand (CA), 16 pockets (best druggability 0.72). MolNFT v1 #90311 on GenesisL1: 3D…
- PDB
- 4EFJ
- Type
- protein + DNA
- Length
- 688 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA target site top strand; DNA target site bottom strand; Laglidadg endonuclease
- EC
- 3.1.-.-
- Ligands
- CA
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | DNA target site top strand | dna | 27 | — | — |
| D, F | DNA target site bottom strand | dna | 26 | — | — |
| A, B | Laglidadg endonuclease (EC 3.1.-.-) | protein | 291 | 48% helix, 20% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains C, D, B, E, F, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.72 | 0.77 | 70 | CA |
| 2 | 120 | 0.63 | 0.88 | 25 | empty |
| 3 | 408 | 0.63 | 0.78 | 37 | empty |
| 4 | 256 | 0.60 | 0.80 | 33 | empty |
| 5 | 278 | 0.59 | 0.79 | 34 | empty |
Interfaces
9 interfaces between chains.
- D–B · 1440 Ų buried · 29 hydrogen bonds · protein-nucleic
- E–A · 1397 Ų buried · 35 hydrogen bonds · protein-nucleic
- F–A · 1381 Ų buried · 29 hydrogen bonds · protein-nucleic
- C–B · 1309 Ų buried · 29 hydrogen bonds · protein-nucleic
- C–D · 1306 Ų buried · 105 hydrogen bonds · nucleic-nucleic
Compared structures
- 4EFJ · Crystal structure of I-GzeII LAGLIDADG homing endonuclease in complex with DNA target site · the same entry in another collection · chain C against C, 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 4EFJ · PDBe 4EFJ
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