Research workbench
Structure of the amidase domain of allophanate hydrolase from pseudomonas sp strain ADP
Analyse Structure of the amidase domain of allophanate hydrolase from pseudomonas sp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CP8
- Type
- protein
- Length
- 2,684 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Allophanate hydrolase
- EC
- 3.5.1.54
- UniProt
- Q936X2
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Allophanate hydrolase (EC 3.5.1.54) | protein | 448 | 41% helix, 17% strand | Q936X2 |
| B, D | Allophanate hydrolase (EC 3.5.1.54) | protein | 447 | 41% helix, 17% strand | Q936X2 |
| E | Allophanate hydrolase (EC 3.5.1.54) | protein | 450 | 42% helix, 16% strand | Q936X2 |
| F | Allophanate hydrolase (EC 3.5.1.54) | protein | 444 | 41% helix, 17% strand | Q936X2 |
Ligands and binding sites
- MLI · Malonate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.82 | 0.84 | 82 | empty |
| 2 | 1019 | 0.76 | 0.78 | 81 | empty |
| 3 | 945 | 0.75 | 0.78 | 73 | empty |
| 4 | 1061 | 0.74 | 0.77 | 75 | empty |
| 5 | 584 | 0.66 | 0.77 | 54 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1220 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1208 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1189 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 539 Ų buried · 2 hydrogen bonds · protein-protein
- C–E · 443 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4CP8 · Structure of the amidase domain of allophanate hydrolase from Pseudomonas sp strain ADP · the same entry in another collection · chain F against F, TM-score 1.00
- Q936X2 · AlphaFold monomer V2.0 prediction for allophanate hydrolase (Q936X2) · a predicted model of the same protein · chain D 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 Q936X2
- Elsewhere: RCSB PDB 4CP8 · PDBe 4CP8 · UniProt Q936X2
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