Research workbench
Structures and dynamics of mesophilic variants from the homing endonuclease I-dmoi
Analyse Structures and dynamics of mesophilic variants from the homing endonuclease… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O6I
- 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; DNA (25-mer)
- EC
- 3.1.-.-
- UniProt
- P21505
- Ligands
- MN, CL
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 191 | 50% helix, 24% strand | P21505 |
| C, G, L | DNA (25-mer) | dna | 25 | — | — |
| D, I, N | DNA (25-mer) | dna | 25 | — | — |
| F, K | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 179 | 51% helix, 26% strand | P21505 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, C, D, F, G, I, K, L, N
- CL · Chloride ion · ion · 2 copies · chains A, G, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.69 | 0.77 | 76 | empty |
| 2 | 155 | 0.49 | 0.78 | 25 | empty |
| 3 | 132 | 0.40 | 0.74 | 21 | empty |
| 4 | 79 | 0.35 | 0.76 | 18 | empty |
| 5 | 102 | 0.34 | 0.74 | 23 | empty |
Interfaces
12 interfaces between chains.
- F–I · 1317 Ų buried · 36 hydrogen bonds · protein-nucleic
- A–D · 1301 Ų buried · 35 hydrogen bonds · protein-nucleic
- K–N · 1289 Ų buried · 35 hydrogen bonds · protein-nucleic
- A–C · 1286 Ų buried · 31 hydrogen bonds · protein-nucleic
- C–D · 1259 Ų buried · 130 hydrogen bonds · nucleic-nucleic
Compared structures
- 5O6I · Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI · the same entry in another collection · chain N against N, TM-score 1.00
- P21505 · AlphaFold monomer V2.0 prediction for homing endonuclease I-dmoi (P21505) · a predicted model of the same protein · chain F against A, 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 5O6I · PDBe 5O6I · UniProt P21505
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