Research workbench
R54A mutant of E9 DNase domain in complex with IM9
Analyse R54A mutant of E9 DNase domain in complex with IM9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VLP
- Type
- protein
- Length
- 216 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colicin-E9 immunity protein; Colicin E9
- UniProt
- P13479, P09883
- Pockets
- 2 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Colicin-E9 immunity protein | protein | 82 | 59% helix, 2% strand | P13479 |
| B | Colicin E9 | protein | 134 | 45% helix, 16% strand | P09883 |
Ligands and binding sites
- MLA · Malonic acid · additive · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.39 | 0.76 | 16 | empty |
| 2 | 56 | 0.33 | 0.77 | 11 | MLA |
Interfaces
1 interface between chains.
- A–B · 809 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2VLP · R54A mutant of E9 DNase domain in complex with Im9 · the same entry in another collection · chain A against A, TM-score 1.00
- P13479 · AlphaFold monomer V2.0 prediction for colicin-E9 immunity protein (P13479) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P09883 · AlphaFold monomer V2.0 prediction for colicin-E9 (P09883) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P13479
- Every structure of UniProt P09883
- Elsewhere: RCSB PDB 2VLP · PDBe 2VLP · UniProt P13479 · UniProt P09883
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