MolNFT v1 · #166621 · protein + DNA
Engineered variant of I-onui meganuclease with improved thermostability
6UVW · I-onui-E-therm: “Engineered variant of I-onui meganuclease with improved thermostability”. X-ray diffraction, 1 ligand (CA), 14 pockets (best druggability 0.64). MolNFT v1 #166621 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6UVW
- Type
- protein + DNA
- Length
- 699 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- I-onui-E-therm; DNA (27-mer)
- Ligands
- CA
- Pockets
- 14 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | I-onui-E-therm | protein | 295 | 51% helix, 22% strand | — |
| B, E | DNA (27-mer) | dna | 27 | — | — |
| C, F | DNA (27-mer) | dna | 27 | — | — |
| D | I-onui-E-therm | protein | 296 | 50% helix, 22% strand | — |
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
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.64 | 0.78 | 65 | empty |
| 2 | 138 | 0.63 | 0.87 | 30 | empty |
| 3 | 186 | 0.61 | 0.83 | 28 | empty |
| 4 | 331 | 0.60 | 0.78 | 51 | CA |
| 5 | 70 | 0.47 | 0.84 | 16 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1674 Ų buried · 28 hydrogen bonds · protein-nucleic
- D–E · 1538 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–C · 1485 Ų buried · 38 hydrogen bonds · protein-nucleic
- D–F · 1381 Ų buried · 35 hydrogen bonds · protein-nucleic
- E–F · 1310 Ų buried · 108 hydrogen bonds · nucleic-nucleic
Compared structures
- 6UVW · Engineered variant of I-OnuI meganuclease with improved thermostability · 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 6UVW · PDBe 6UVW
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