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Structure of the D53,54N mutant of histidine decarboxylase bound with histidine methyl ester at 25 C
Analyse Structure of the D53,54N mutant of histidine decarboxylase bound with histidine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IBW
- Type
- protein
- Length
- 927 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidine decarboxylase beta chain; Histidine decarboxylase alpha chain
- EC
- 4.1.1.22
- UniProt
- P00862
- Ligands
- PYR, PVH
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 26% 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 (EC 4.1.1.22) | protein | 228 | 27% helix, 34% strand | P00862 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 3 copies · chains A, B, C, D, E, F
- 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 | 708 | 0.75 | 0.80 | 95 | PYR, 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 · 3206 Ų buried · 71 hydrogen bonds · protein-protein
- A–B · 3203 Ų buried · 72 hydrogen bonds · protein-protein
- E–F · 3202 Ų buried · 72 hydrogen bonds · protein-protein
- D–E · 946 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 927 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
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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