MolNFT v2 · #9952 · protein
Structure of the D53,54N mutant of histidine decarboxylase bound with histidine methyl ester at 25 C
1IBW · Histidine decarboxylase beta chain: “Structure of the D53,54N mutant of histidine decarboxylase bound with histidine methyl ester at 25 C”. X-ray diffraction at 3.2, 1 ligand (PVH), 11 pockets (best druggability 0.72). MolNFT v2…
- PDB
- 1IBW
- Type
- protein
- Length
- 930 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Lactobacillus sp. 30A
- Molecule
- Histidine decarboxylase beta chain; Histidine decarboxylase alpha chain
- EC
- 4.1.1.22
- UniProt
- P00862
- Ligands
- PVH
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · resolution 3.2 · 2 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Histidine decarboxylase beta chain (EC 4.1.1.22) | protein | 81 | 22% helix, 27% strand | P00862 |
| B, D, F | Histidine decarboxylase alpha chain | protein | 229 | 27% helix, 34% strand | P00862 |
Ligands and binding sites
- PVH · Histidine-methyl-ester · 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
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.72 | 0.79 | 95 | PVH |
| 2 | 150 | 0.53 | 0.81 | 52 | empty |
| 3 | 109 | 0.48 | 0.80 | 24 | empty |
| 4 | 106 | 0.47 | 0.80 | 23 | empty |
| 5 | 99 | 0.46 | 0.80 | 23 | empty |
Interfaces
15 interfaces between chains.
- C–D · 3230 Ų buried · 71 hydrogen bonds · protein-protein
- A–B · 3226 Ų buried · 72 hydrogen bonds · protein-protein
- E–F · 3225 Ų buried · 72 hydrogen bonds · protein-protein
- D–E · 953 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 934 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 3 modified (covalent ligand, nonstandard).
Compared structures
- 1IBW · Structure of the D53,54N mutant of histidine decarboxylase bound with histidine methyl… · the same entry in another collection · chain A against A, 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 1IBW · PDBe 1IBW · UniProt P00862
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