Research workbench
K262A mutant of I-smami
Analyse K262A 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
- 5E63
- Type
- protein + DNA
- Length
- 343 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- I-smami laglidadg meganuclease; DNA right half site bottom strand; DNA left half site…
- UniProt
- F7WD42
- Ligands
- MG
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | I-smami laglidadg meganuclease | protein | 293 | 49% helix, 21% strand | F7WD42 |
| B | DNA right half site bottom strand | dna | 14 | — | — |
| C | DNA left half site bottom strand | dna | 11 | — | — |
| D | DNA left site top strand | dna | 15 | — | — |
| E | 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, E
- MXE · 2-methoxyethanol · additive · chains A
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains B, E
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 | 184 | 0.62 | 0.84 | 31 | MG |
| 2 | 145 | 0.43 | 0.76 | 25 | empty |
| 3 | 55 | 0.41 | 0.82 | 18 | empty |
| 4 | 74 | 0.38 | 0.78 | 20 | empty |
| 5 | 79 | 0.34 | 0.75 | 17 | empty |
Interfaces
10 interfaces between chains.
- A–D · 1068 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–B · 926 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–C · 629 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–D · 576 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- B–E · 559 Ų buried · 45 hydrogen bonds · nucleic-nucleic
Compared structures
- 5E63 · K262A 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 5E63 · PDBe 5E63 · UniProt F7WD42
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