MolNFT v1 · #69354 · protein + DNA
I-msoi re-designed for altered DNA cleavage specificity (-7C)
3KO2 · Site-specific DNA endonuclease I-msoi: “I-msoi re-designed for altered DNA cleavage specificity (-7C)”. X-ray diffraction, 1 ligand (CA), 12 pockets (best druggability 0.73). MolNFT v1 #69354 on GenesisL1: 3D structure, binding…
- PDB
- 3KO2
- Type
- protein + DNA
- Length
- 740 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Site-specific DNA endonuclease I-msoi; 5'-D(*GP*CP*AP*GP*AP*CP*CP*GP*TP*CP*GP*TP*GP*AP*GP*…
- UniProt
- C0JWR6
- Ligands
- CA
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F, G | Site-specific DNA endonuclease I-msoi | protein | 161 | 51% helix, 19% strand | C0JWR6 |
| C, H | 5'-D(*GP*CP*AP*GP*AP*CP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP *GP*TP*TP*CP*CP*G)-3' | dna | 24 | — | — |
| D, I | 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP *GP*TP*CP*TP*GP*C)-3' | dna | 24 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, F, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.73 | 0.77 | 82 | CA |
| 2 | 607 | 0.68 | 0.78 | 67 | CA |
| 3 | 395 | 0.64 | 0.79 | 47 | CA |
| 4 | 325 | 0.64 | 0.81 | 37 | CA |
| 5 | 60 | 0.61 | 0.92 | 19 | empty |
Interfaces
15 interfaces between chains.
- H–I · 1163 Ų buried · 81 hydrogen bonds · nucleic-nucleic
- C–D · 1158 Ų buried · 91 hydrogen bonds · nucleic-nucleic
- F–G · 1085 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1063 Ų buried · 13 hydrogen bonds · protein-protein
- F–H · 817 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 3KO2 · I-MsoI re-designed for altered DNA cleavage specificity (-7C) · 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 C0JWR6
- Elsewhere: RCSB PDB 3KO2 · PDBe 3KO2 · UniProt C0JWR6
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