Research workbench
I-msoi re-designed for altered DNA cleavage specificity (-8GCG)
Analyse I-msoi re-designed for altered DNA cleavage specificity (-8GCG) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MIP
- Type
- protein + DNA
- Length
- 370 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mso-8G; DNA (5'- D(*GP*CP*AP*GP*GP*CP*GP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*CP*GP*CP*TP*CP*…
- Ligands
- CA
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mso-8G | protein | 161 | 53% helix, 19% strand | — |
| C | DNA (5'- D(*GP*CP*AP*GP*GP*CP*GP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*CP*GP*CP*TP*CP* CP*G)-3') | dna | 24 | — | — |
| D | DNA (5'- D(*CP*GP*GP*AP*GP*CP*GP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*CP*GP*CP*CP*TP* GP*C)-3') | dna | 24 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.62 | 0.80 | 34 | CA |
| 2 | 326 | 0.62 | 0.79 | 34 | empty |
| 3 | 74 | 0.32 | 0.75 | 21 | empty |
| 4 | 57 | 0.29 | 0.75 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1197 Ų buried · 115 hydrogen bonds · nucleic-nucleic
- A–B · 1019 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 859 Ų buried · 27 hydrogen bonds · protein-nucleic
- B–D · 848 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–C · 749 Ų buried · 23 hydrogen bonds · protein-nucleic
Compared structures
- 3MIP · I-MsoI re-designed for altered DNA cleavage specificity (-8GCG) · 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 3MIP · PDBe 3MIP
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.