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
- 5O6G
- Type
- protein + DNA
- Length
- 694 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
- 12 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 188 | 47% helix, 24% strand | P21505 |
| B, E, H | DNA (25-mer) | dna | 25 | — | — |
| C, F, I | DNA (25-mer) | dna | 25 | — | — |
| D, G | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 178 | 49% helix, 26% strand | P21505 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F, G, H, I
- CL · Chloride ion · ion · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.56 | 0.76 | 30 | empty |
| 2 | 319 | 0.56 | 0.76 | 28 | empty |
| 3 | 275 | 0.53 | 0.76 | 28 | empty |
| 4 | 141 | 0.41 | 0.75 | 27 | empty |
| 5 | 131 | 0.40 | 0.75 | 20 | empty |
Interfaces
15 interfaces between chains.
- A–B · 1323 Ų buried · 35 hydrogen bonds · protein-nucleic
- A–C · 1322 Ų buried · 35 hydrogen bonds · protein-nucleic
- D–F · 1316 Ų buried · 38 hydrogen bonds · protein-nucleic
- G–I · 1309 Ų buried · 33 hydrogen bonds · protein-nucleic
- B–C · 1276 Ų buried · 131 hydrogen bonds · nucleic-nucleic
Compared structures
- 5O6G · Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI · the same entry in another collection · chain C against C, TM-score 1.00
- P21505 · AlphaFold monomer V2.0 prediction for homing endonuclease I-dmoi (P21505) · a predicted model of the same protein · chain D 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 5O6G · PDBe 5O6G · UniProt P21505
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