MolNFT v1 · #134856 · protein + DNA
Engineered variant of I-onui meganuclease targeting the HIV CCR5 gene; harbors 43 point mutations relative to wild-type I-onui
5THG · I-ONUI_E-HCCR5: “Engineered variant of I-onui meganuclease targeting the HIV CCR5 gene; harbors 43 point mutations relative to…”. X-ray diffraction, 1 ligand (CA), 10 pockets (best druggability 0.61). MolNFT v1 #134856 on GenesisL1…
- PDB
- 5THG
- Type
- protein + DNA
- Length
- 698 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- I-ONUI_E-HCCR5; DNA (29-mer)
- Ligands
- CA
- Pockets
- 10 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | I-ONUI_E-HCCR5 | protein | 294 | 48% helix, 19% strand | — |
| B, E | DNA (29-mer) | dna | 28 | — | — |
| C | DNA (29-mer) | dna | 28 | — | — |
| D | I-ONUI_E-HCCR5 | protein | 291 | 47% helix, 19% strand | — |
| F | DNA (29-mer) | dna | 29 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 2 copies · chains B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.61 | 0.84 | 33 | empty |
| 2 | 143 | 0.60 | 0.85 | 26 | CA |
| 3 | 128 | 0.60 | 0.85 | 31 | empty |
| 4 | 72 | 0.59 | 0.89 | 23 | CA |
| 5 | 229 | 0.58 | 0.80 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1580 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–B · 1518 Ų buried · 30 hydrogen bonds · protein-nucleic
- D–F · 1490 Ų buried · 29 hydrogen bonds · protein-nucleic
- D–E · 1446 Ų buried · 26 hydrogen bonds · protein-nucleic
- E–F · 1352 Ų buried · 96 hydrogen bonds · nucleic-nucleic
Compared structures
- 5THG · Engineered variant of I-OnuI meganuclease targeting the HIV CCR5 gene; harbors 43 point… · 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 5THG · PDBe 5THG
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