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
- 2XE0
- Type
- protein + DNA
- Length
- 352 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- I-crei V2V3 variant; 24MER DNA
- Ligands
- MG
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | I-crei V2V3 variant | protein | 152 | 50% helix, 21% strand | — |
| B | I-crei V2V3 variant | protein | 152 | 53% helix, 21% strand | — |
| C | 24MER DNA | dna | 24 | — | — |
| D | 24MER DNA | dna | 24 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, B, C
- PGO · S-1,2-propanediol · additive · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.68 | 0.92 | 19 | empty |
| 2 | 60 | 0.67 | 0.95 | 19 | empty |
| 3 | 57 | 0.58 | 0.91 | 17 | empty |
| 4 | 81 | 0.45 | 0.81 | 19 | empty |
| 5 | 65 | 0.42 | 0.82 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1203 Ų buried · 102 hydrogen bonds · nucleic-nucleic
- B–C · 1017 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–B · 933 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 929 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–D · 897 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 2XE0 · 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 2XE0 · PDBe 2XE0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.