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The crystal structure of I-dmoi in complex with its target DNA at 2 days incubation in 5MM mn (state 4)
Analyse The crystal structure of I-dmoi in complex with its target DNA at 2 days… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UNA
- Type
- protein + DNA
- Length
- 694 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homing endonuclease I-dmoi; 25MER; 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3'…
- EC
- 3.1.-.-
- UniProt
- P21505
- Ligands
- MN
- Pockets
- 12 · best druggability 0.59
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 184 | 49% helix, 25% strand | P21505 |
| B, E, H | 25MER | dna | 25 | — | — |
| C, F, I | 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3' | dna | 15 | — | — |
| G | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 176 | 50% helix, 26% strand | P21505 |
| K, M, O | 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*C)-3' | dna | 10 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 9 copies · chains A, B, K, C, D, E, F, M, G, H, O, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.59 | 0.76 | 27 | empty |
| 2 | 323 | 0.56 | 0.76 | 30 | empty |
| 3 | 157 | 0.44 | 0.75 | 23 | empty |
| 4 | 152 | 0.41 | 0.74 | 26 | empty |
| 5 | 150 | 0.40 | 0.74 | 30 | empty |
Interfaces
24 interfaces between chains.
- D–E · 1302 Ų buried · 38 hydrogen bonds · protein-nucleic
- A–B · 1281 Ų buried · 36 hydrogen bonds · protein-nucleic
- G–H · 1268 Ų buried · 37 hydrogen bonds · protein-nucleic
- A–C · 1062 Ų buried · 29 hydrogen bonds · protein-nucleic
- D–F · 1046 Ų buried · 28 hydrogen bonds · protein-nucleic
Compared structures
- 4UNA · The crystal structure of I-dmoi in complex with its target DNA at 2 days incubation in… · the same entry in another collection · chain O against O, 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 4UNA · PDBe 4UNA · UniProt P21505
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