Research workbench
K103A/K262A double mutant of I-smami
Analyse K103A/K262A double mutant of I-smami in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E67
- Type
- protein + DNA
- Length
- 344 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- I-smami laglidadg meganuclease; DNA bottom strand; DNA top strand
- UniProt
- F7WD42
- Ligands
- MG
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | I-smami laglidadg meganuclease | protein | 294 | 49% helix, 21% strand | F7WD42 |
| B | DNA bottom strand | dna | 25 | — | — |
| C | DNA top strand | dna | 25 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B, C
- MXE · 2-methoxyethanol · additive · chains A, B, C
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.77 | 0.85 | 62 | MXE |
| 2 | 138 | 0.42 | 0.76 | 16 | empty |
| 3 | 65 | 0.36 | 0.78 | 19 | empty |
| 4 | 70 | 0.33 | 0.76 | 18 | empty |
| 5 | 55 | 0.28 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1433 Ų buried · 29 hydrogen bonds · protein-nucleic
- A–C · 1417 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–C · 1170 Ų buried · 96 hydrogen bonds · nucleic-nucleic
Compared structures
- 5E67 · K103A/K262A double mutant of I-SmaMI · the same entry in another collection · chain A 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 F7WD42
- Elsewhere: RCSB PDB 5E67 · PDBe 5E67 · UniProt F7WD42
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