Research workbench
Amide receptor of the amidase operon of pseudomonas aeruginosa (amic) complexed with the negative regulator amir.
Analyse Amide receptor of the amidase operon of pseudomonas aeruginosa (amic) complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QO0
- Type
- protein
- Length
- 1,130 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amic; Amir
- UniProt
- P27017, P10932
- Ligands
- BMD
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amic | protein | 373 | 43% helix, 20% strand | P27017 |
| B | Amic | protein | 374 | 42% helix, 20% strand | P27017 |
| D | Amir | protein | 189 | 59% helix, 13% strand | P10932 |
| E | Amir | protein | 194 | 59% helix, 13% strand | P10932 |
Ligands and binding sites
- BMD · Butyramide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.80 | 0.82 | 108 | empty |
| 2 | 102 | 0.61 | 0.88 | 30 | empty |
| 3 | 185 | 0.53 | 0.78 | 25 | empty |
| 4 | 76 | 0.52 | 0.85 | 19 | empty |
| 5 | 135 | 0.47 | 0.78 | 26 | empty |
Interfaces
6 interfaces between chains.
- D–E · 2132 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 605 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 593 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 523 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 517 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1QO0 · Amide receptor of the amidase operon of Pseudomonas aeruginosa (AmiC) complexed with the… · the same entry in another collection · chain E against E, TM-score 1.00
- P27017 · AlphaFold monomer V2.0 prediction for aliphatic amidase expression- regulating protein… · a predicted model of the same protein · chain A against A, TM-score 1.00
- P10932 · AlphaFold monomer V2.0 prediction for aliphatic amidase regulator (P10932) · a predicted model of the same protein · chain E against A, TM-score 0.93
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 P27017
- Every structure of UniProt P10932
- Elsewhere: RCSB PDB 1QO0 · PDBe 1QO0 · UniProt P27017 · UniProt P10932
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