Research workbench
I-smami K103A mutant
Analyse I-smami K103A mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E5S
- Type
- protein + DNA
- Length
- 347 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- I-smami laglidadg meganuclease; Bottom strand DNA; Top strand DNA left site; DNA…
- UniProt
- F7WD42
- Ligands
- MG
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | I-smami laglidadg meganuclease | protein | 297 | 48% helix, 22% strand | F7WD42 |
| B | Bottom strand DNA | dna | 25 | — | — |
| C | Top strand DNA left site | dna | 15 | — | — |
| D | DNA (5'-D(P*CP*AP*GP*GP*TP*GP*TP*AP*CP*G)-3') | dna | 10 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, D
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains B, D
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 | 87 | 0.57 | 0.87 | 23 | empty |
| 2 | 122 | 0.47 | 0.79 | 14 | MG |
| 3 | 103 | 0.40 | 0.77 | 22 | empty |
| 4 | 103 | 0.36 | 0.75 | 14 | empty |
| 5 | 70 | 0.33 | 0.76 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1462 Ų buried · 29 hydrogen bonds · protein-nucleic
- A–C · 1031 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 750 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- A–D · 603 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–D · 527 Ų buried · 38 hydrogen bonds · nucleic-nucleic
Compared structures
- 5E5S · I-SmaMI K103A mutant · 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 5E5S · PDBe 5E5S · UniProt F7WD42
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