MolNFT v1 · #76638 · protein + DNA
Crystal structure of a novel laglidadg homing endonuclease, I-onui (from ophiostoma novo-ulmi subsp. americana)
3QQY · Ribosomal protein 3/HOMING endonuclease-like protein fusion: “Crystal structure of a novel laglidadg homing endonuclease, I-onui (from ophiostoma novo-ulmi subsp.…”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability…
- PDB
- 3QQY
- Type
- protein + DNA
- Length
- 351 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal protein 3/HOMING endonuclease-like protein fusion; DNA (26-mer)
- UniProt
- Q4VWW5
- Ligands
- MG
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal protein 3/HOMING endonuclease-like protein fusion | protein | 299 | 49% helix, 22% strand | Q4VWW5 |
| B | DNA (26-mer) | dna | 26 | — | — |
| C | DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.71 | 0.99 | 22 | empty |
| 2 | 63 | 0.64 | 0.94 | 22 | empty |
| 3 | 151 | 0.63 | 0.86 | 24 | empty |
| 4 | 224 | 0.51 | 0.77 | 31 | empty |
| 5 | 136 | 0.43 | 0.76 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1576 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–C · 1540 Ų buried · 30 hydrogen bonds · protein-nucleic
- B–C · 1253 Ų buried · 104 hydrogen bonds · nucleic-nucleic
Compared structures
- 3QQY · Crystal structure of a novel LAGLIDADG homing endonuclease, I-OnuI (from Ophiostoma… · 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 Q4VWW5
- Elsewhere: RCSB PDB 3QQY · PDBe 3QQY · UniProt Q4VWW5
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