MolNFT v1 · #88256 · protein
Structure of the amidase domain of allophanate hydrolase from pseudomonas sp strain ADP
4CP8: “Structure of the amidase domain of allophanate hydrolase from pseudomonas sp strain ADP”. X-ray diffraction, 18 pockets (best druggability 0.82). MolNFT v1 #88256 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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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