Research workbench
Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus
Analyse Molecular basis of engineered meganuclease targeting of the endogenous human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MX9
- Type
- protein + DNA
- Length
- 346 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein SCV3V2(G19S); DNA (5'- D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*CP*CP*TP*CP*AP*GP…
- Ligands
- CA
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein SCV3V2(G19S) | protein | 298 | 55% helix, 21% strand | — |
| C | DNA (5'- D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*CP*CP*TP*CP*AP*GP*CP*CP*AP* GP*A)-3') | dna | 24 | — | — |
| D | DNA (5'- D(*TP*CP*TP*GP*GP*CP*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*GP*AP*GP*AP*AP*CP* AP*A)-3') | dna | 24 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.64 | 0.90 | 19 | empty |
| 2 | 64 | 0.49 | 0.85 | 19 | empty |
| 3 | 63 | 0.45 | 0.83 | 21 | empty |
| 4 | 73 | 0.40 | 0.80 | 14 | empty |
| 5 | 52 | 0.39 | 0.81 | 8 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1774 Ų buried · 31 hydrogen bonds · protein-nucleic
- A–D · 1601 Ų buried · 32 hydrogen bonds · protein-nucleic
- C–D · 1170 Ų buried · 88 hydrogen bonds · nucleic-nucleic
Compared structures
- 3MX9 · Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus · 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 3MX9 · PDBe 3MX9
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