Research workbench
The crystal structure of I-dmoi in complex with its target DNA at 6 days incubation in 5MM mn (state 5)
Analyse The crystal structure of I-dmoi in complex with its target DNA at 6 days… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UNB
- Type
- protein + DNA
- Length
- 692 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homing endonuclease I-dmoi; 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*A)-3'…
- EC
- 3.1.-.-
- UniProt
- P21505
- Ligands
- MN
- Pockets
- 13 · best druggability 0.58
Structure
x-ray diffraction · 7 distinct chains · 49% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 183 | 49% helix, 25% strand | P21505 |
| B, E, H | 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*A)-3' | dna | 14 | — | — |
| C, F, I | 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3' | dna | 15 | — | — |
| D | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 184 | 48% helix, 26% strand | P21505 |
| G | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 175 | 49% helix, 26% strand | P21505 |
| J, L, N | 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*G)-3' | dna | 11 | — | — |
| 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 · 10 copies · chains A, B, K, C, J, D, E, M, F, L, G, H, O, I, N
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 | 384 | 0.58 | 0.76 | 29 | empty |
| 2 | 310 | 0.57 | 0.77 | 31 | empty |
| 3 | 206 | 0.48 | 0.76 | 25 | empty |
| 4 | 149 | 0.40 | 0.74 | 23 | empty |
| 5 | 90 | 0.38 | 0.76 | 13 | empty |
Interfaces
36 interfaces between chains.
- D–F · 1032 Ų buried · 28 hydrogen bonds · protein-nucleic
- G–I · 1016 Ų buried · 29 hydrogen bonds · protein-nucleic
- A–C · 999 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–B · 808 Ų buried · 21 hydrogen bonds · protein-nucleic
- D–E · 798 Ų buried · 21 hydrogen bonds · protein-nucleic
Compared structures
- 4UNB · The crystal structure of I-dmoi in complex with its target DNA at 6 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 4UNB · PDBe 4UNB · UniProt P21505
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