MolNFT v1 · #107793 · protein + DNA
The crystal structure of I-dmoi in complex with its target DNA at 1H incubation in 5MM mn (state 2)
4UN8 · Homing endonuclease I-dmoi: “The crystal structure of I-dmoi in complex with its target DNA at 1H incubation in 5MM mn (state 2)”. X-ray diffraction, 1 ligand (MN), 15 pockets (best druggability 0.59). MolNFT v1 #107793 on…
- PDB
- 4UN8
- Type
- protein + DNA
- Length
- 702 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homing endonuclease I-dmoi; 25MER
- EC
- 3.1.-.-
- UniProt
- P21505
- Ligands
- MN
- Pockets
- 15 · best druggability 0.59
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 184 | 48% helix, 25% strand | P21505 |
| B, E, H | 25MER | dna | 25 | — | — |
| C, F, I | 25MER | dna | 25 | — | — |
| D | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 191 | 46% helix, 24% strand | P21505 |
| G | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 177 | 50% helix, 25% strand | P21505 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.59 | 0.76 | 27 | empty |
| 2 | 254 | 0.55 | 0.77 | 27 | empty |
| 3 | 193 | 0.54 | 0.79 | 26 | empty |
| 4 | 192 | 0.48 | 0.76 | 23 | empty |
| 5 | 168 | 0.43 | 0.74 | 30 | empty |
Interfaces
15 interfaces between chains.
- G–I · 1334 Ų buried · 38 hydrogen bonds · protein-nucleic
- A–C · 1326 Ų buried · 39 hydrogen bonds · protein-nucleic
- D–F · 1324 Ų buried · 35 hydrogen bonds · protein-nucleic
- D–E · 1277 Ų buried · 34 hydrogen bonds · protein-nucleic
- E–F · 1265 Ų buried · 129 hydrogen bonds · nucleic-nucleic
Compared structures
- 4UN8 · The crystal structure of I-dmoi in complex with its target DNA at 1H incubation in 5MM mn… · the same entry in another collection · chain I against I, TM-score 1.00
- P21505 · AlphaFold monomer V2.0 prediction for homing endonuclease I-dmoi (P21505) · a predicted model of the same protein · chain G 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 P21505
- Elsewhere: RCSB PDB 4UN8 · PDBe 4UN8 · UniProt P21505
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.