Research workbench
Domain III of pseudomonas aeruginosa exotoxin complexed with nicotinamide and AMP
Analyse Domain III of pseudomonas aeruginosa exotoxin complexed with nicotinamide and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DMA
- Type
- protein
- Length
- 393 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exotoxin a
- UniProt
- P11439
- Ligands
- NCA, AMP
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exotoxin a | protein | 204 | 26% helix, 24% strand | P11439 |
| B | Exotoxin a | protein | 189 | 28% helix, 22% strand | P11439 |
Ligands and binding sites
- NCA · Nicotinamide · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.60 | 0.78 | 47 | empty |
| 2 | 274 | 0.53 | 0.76 | 28 | empty |
| 3 | 75 | 0.42 | 0.80 | 12 | empty |
| 4 | 107 | 0.42 | 0.76 | 21 | NCA, AMP |
| 5 | 61 | 0.38 | 0.79 | 14 | NCA |
Interfaces
1 interface between chains.
- A–B · 973 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1DMA · Domain III of pseudomonas aeruginosa exotoxin complexed with nicotinamide and AMP · the same entry in another collection · chain A against A, TM-score 1.00
- P11439 · AlphaFold monomer V2.0 prediction for exotoxin a (P11439) · a predicted model of the same protein · chain A 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 P11439
- Elsewhere: RCSB PDB 1DMA · PDBe 1DMA · UniProt P11439
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