Research workbench
The crystal structure of I-dmoi in complex with its target DNA at 10 days incubation in 5MM mg (state 7)
Analyse The crystal structure of I-dmoi in complex with its target DNA at 10 days… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D6N
- Type
- protein + DNA
- Length
- 701 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homing endonuclease I-dmoi; 5'-D(*DGP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*DAP)-3'…
- EC
- 3.1.-.-
- UniProt
- P21505
- Ligands
- MG
- Pockets
- 12 · best druggability 0.54
Structure
x-ray diffraction · 7 distinct chains · 49% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 183 | 48% helix, 25% strand | P21505 |
| B, G, L | 5'-D(*DGP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*DAP)-3' | dna | 14 | — | — |
| C, H, M | 5'-D(*DGP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3' | dna | 11 | — | — |
| D, I, N | 5'-D(*DCP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*DAP*C)-3' | dna | 15 | — | — |
| E, J, O | 5'-D(*DCP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3' | dna | 10 | — | — |
| F | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 191 | 50% helix, 24% strand | P21505 |
| K | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 177 | 49% helix, 26% strand | P21505 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, C, D, B, E, F, G, J, H, I, K, M, N, L, O
- ACT · Acetate ion · additive · 3 copies · chains A, F
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 | 270 | 0.54 | 0.76 | 32 | empty |
| 2 | 297 | 0.54 | 0.75 | 28 | empty |
| 3 | 61 | 0.48 | 0.84 | 13 | ACT |
| 4 | 163 | 0.42 | 0.74 | 28 | ACT |
| 5 | 102 | 0.41 | 0.76 | 18 | ACT |
Interfaces
33 interfaces between chains.
- F–I · 1039 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–D · 975 Ų buried · 25 hydrogen bonds · protein-nucleic
- K–N · 974 Ų buried · 26 hydrogen bonds · protein-nucleic
- F–G · 824 Ų buried · 24 hydrogen bonds · protein-nucleic
- K–L · 793 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 4D6N · The crystal structure of I-dmoi in complex with its target DNA at 10 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 4D6N · PDBe 4D6N · UniProt P21505
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