Research workbench
Human histidine decarboxylase mutant Y334F soaking with histidine
Analyse Human histidine decarboxylase mutant Y334F soaking with histidine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EIY
- Type
- protein
- Length
- 933 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidine decarboxylase
- EC
- 4.1.1.22
- UniProt
- P19113
- Ligands
- PLP, HIS, SO4
- Pockets
- 12 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidine decarboxylase (EC 4.1.1.22) | protein | 467 | 49% helix, 13% strand | P19113 |
| B | Histidine decarboxylase (EC 4.1.1.22) | protein | 466 | 51% helix, 14% strand | P19113 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- HIS · Histidine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.67 | 0.82 | 56 | PLP, HIS |
| 2 | 295 | 0.64 | 0.81 | 45 | PLP, HIS |
| 3 | 137 | 0.49 | 0.79 | 23 | empty |
| 4 | 113 | 0.47 | 0.79 | 25 | empty |
| 5 | 137 | 0.43 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 6070 Ų buried · 83 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 7EIY · Human histidine decarboxylase mutant Y334F soaking with histidine · the same entry in another collection · chain A against A, TM-score 1.00
- P19113 · AlphaFold monomer V2.0 prediction for histidine decarboxylase (P19113) · a predicted model of the same protein · chain B 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 P19113
- Elsewhere: RCSB PDB 7EIY · PDBe 7EIY · UniProt P19113
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