MolNFT v1 · #88818 · protein + DNA
The crystal structure of I-dmoi in complex with its target DNA at 1H incubation in 5MM mg (state 2)
4D6O · Homing endonuclease I-dmoi: “The crystal structure of I-dmoi in complex with its target DNA at 1H incubation in 5MM mg (state 2)”. X-ray diffraction, 1 ligand (MG), 15 pockets (best druggability 0.54). MolNFT v1 #88818 on GenesisL1…
- PDB
- 4D6O
- Type
- protein + DNA
- Length
- 699 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
- MG
- Pockets
- 15 · best druggability 0.54
Structure
x-ray diffraction · 7 distinct chains · 50% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 182 | 49% helix, 25% strand | P21505 |
| B, H | 25MER | dna | 25 | — | — |
| C, I | 25MER | dna | 25 | — | — |
| D | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 191 | 50% helix, 24% strand | P21505 |
| E | 25MER | dna | 25 | — | — |
| F | 25MER | dna | 25 | — | — |
| G | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 176 | 50% helix, 26% strand | P21505 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F, G, H, I
- ACT · Acetate ion · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.54 | 0.76 | 31 | empty |
| 2 | 283 | 0.53 | 0.76 | 29 | empty |
| 3 | 72 | 0.50 | 0.84 | 19 | ACT |
| 4 | 180 | 0.46 | 0.75 | 22 | empty |
| 5 | 164 | 0.42 | 0.74 | 29 | empty |
Interfaces
15 interfaces between chains.
- A–C · 1317 Ų buried · 33 hydrogen bonds · protein-nucleic
- D–F · 1314 Ų buried · 35 hydrogen bonds · protein-nucleic
- G–I · 1313 Ų buried · 34 hydrogen bonds · protein-nucleic
- D–E · 1295 Ų buried · 32 hydrogen bonds · protein-nucleic
- G–H · 1262 Ų buried · 34 hydrogen bonds · protein-nucleic
Compared structures
- 4D6O · The crystal structure of I-dmoi in complex with its target DNA at 1H incubation in 5MM mg… · 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 0.99
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 4D6O · PDBe 4D6O · UniProt P21505
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