MolNFT v1 · #9242 · protein
Structure of pyruvoyl-dependent histidine decarboxylase at pH 8
1HQ6: “Structure of pyruvoyl-dependent histidine decarboxylase at pH 8”. X-ray diffraction, 1 ligand (PYR), 8 pockets (best druggability 0.53). MolNFT v1 #9242 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1HQ6
- Type
- protein
- Length
- 588 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidine decarboxylase
- EC
- 4.1.1.22
- UniProt
- P00862
- Ligands
- PYR
- Pockets
- 8 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Histidine decarboxylase (EC 4.1.1.22) | protein | 66 | 15% helix, 30% strand | P00862 |
| B, D | Histidine decarboxylase (EC 4.1.1.22) | protein | 228 | 26% helix, 36% strand | P00862 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.53 | 0.84 | 21 | empty |
| 2 | 99 | 0.49 | 0.82 | 22 | empty |
| 3 | 84 | 0.42 | 0.79 | 20 | empty |
| 4 | 56 | 0.40 | 0.81 | 15 | empty |
| 5 | 90 | 0.34 | 0.74 | 14 | empty |
Interfaces
5 interfaces between chains.
- C–D · 3099 Ų buried · 66 hydrogen bonds · protein-protein
- A–B · 3088 Ų buried · 68 hydrogen bonds · protein-protein
- B–D · 222 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 147 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 142 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1HQ6 · Structure of pyruvoyl-dependent histidine decarboxylase at pH 8 · the same entry in another collection · chain D against D, TM-score 1.00
- P00862 · AlphaFold monomer V2.0 prediction for histidine decarboxylase proenzyme (P00862) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 1HQ6 · PDBe 1HQ6 · UniProt P00862
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