MolNFT v1 · #107794 · protein + DNA
The crystal structure of I-dmoi in complex with its target DNA at 8H incubation in 5MM mn (state 3)
4UN9 · Homing endonuclease I-dmoi: “The crystal structure of I-dmoi in complex with its target DNA at 8H incubation in 5MM mn (state 3)”. X-ray diffraction, 1 ligand (MN), 13 pockets (best druggability 0.56). MolNFT v1 #107794 on…
- PDB
- 4UN9
- 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
- 13 · best druggability 0.56
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 | 47% helix, 25% strand | P21505 |
| G | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 177 | 50% helix, 26% strand | P21505 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 10 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
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.56 | 0.76 | 26 | empty |
| 2 | 272 | 0.53 | 0.76 | 25 | empty |
| 3 | 202 | 0.49 | 0.76 | 21 | empty |
| 4 | 161 | 0.44 | 0.75 | 29 | empty |
| 5 | 127 | 0.38 | 0.74 | 24 | empty |
Interfaces
15 interfaces between chains.
- G–I · 1354 Ų buried · 42 hydrogen bonds · protein-nucleic
- A–C · 1354 Ų buried · 37 hydrogen bonds · protein-nucleic
- D–F · 1297 Ų buried · 34 hydrogen bonds · protein-nucleic
- G–H · 1266 Ų buried · 38 hydrogen bonds · protein-nucleic
- E–F · 1261 Ų buried · 125 hydrogen bonds · nucleic-nucleic
Compared structures
- 4UN9 · The crystal structure of I-dmoi in complex with its target DNA at 8H 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 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 4UN9 · PDBe 4UN9 · UniProt P21505
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