MolNFT v1 · #18731 · protein
Refined structure of the pyruvoyl-dependent histidine decarboxylase from lactobacillus 30A
1PYA · Pyruvoyl-dependent histidine decarboxylase (L-histidine…: “Refined structure of the pyruvoyl-dependent histidine decarboxylase from lactobacillus 30A”. X-ray diffraction, 1 ligand (PYR), 12 pockets (best druggability 0.76). MolNFT…
- PDB
- 1PYA
- Type
- protein
- Length
- 927 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvoyl-dependent histidine decarboxylase (L-histidine carboxylase)
- EC
- 4.1.1.22
- UniProt
- P00862
- Ligands
- PYR
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Pyruvoyl-dependent histidine decarboxylase (L-histidine carboxylase) (EC 4.1.1.22) | protein | 81 | 27% helix, 27% strand | P00862 |
| B, D, F | Pyruvoyl-dependent histidine decarboxylase (L-histidine carboxylase) (EC 4.1.1.22) | protein | 228 | 27% helix, 36% strand | P00862 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 3 copies · chains A, B, C, D, E, F
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 | 760 | 0.76 | 0.81 | 86 | PYR |
| 2 | 62 | 0.72 | 0.97 | 19 | empty |
| 3 | 117 | 0.50 | 0.80 | 22 | empty |
| 4 | 101 | 0.47 | 0.80 | 22 | empty |
| 5 | 125 | 0.45 | 0.78 | 40 | empty |
Interfaces
15 interfaces between chains.
- E–F · 3253 Ų buried · 67 hydrogen bonds · protein-protein
- C–D · 3242 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 3223 Ų buried · 62 hydrogen bonds · protein-protein
- D–E · 967 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 946 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 1PYA · Refined structure of the pyruvoyl-dependent histidine decarboxylase from lactobacillus 30A · the same entry in another collection · chain F against F, TM-score 1.00
- P00862 · AlphaFold monomer V2.0 prediction for histidine decarboxylase proenzyme (P00862) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P00862
- Elsewhere: RCSB PDB 1PYA · PDBe 1PYA · UniProt P00862
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.