Research workbench
Structure of the D53,54N mutant of histidine decarboxylase at 25 C
Analyse Structure of the D53,54N mutant of histidine decarboxylase at 25 C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IBU
- Type
- protein
- Length
- 886 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
- Pockets
- 12 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidine decarboxylase beta chain (EC 4.1.1.22) | protein | 65 | 11% helix, 28% strand | P00862 |
| B, D, F | Histidine decarboxylase alpha chain (EC 4.1.1.22) | protein | 228 | 27% helix, 35% strand | P00862 |
| C | Histidine decarboxylase beta chain (EC 4.1.1.22) | protein | 67 | 10% helix, 28% strand | P00862 |
| E | Histidine decarboxylase beta chain (EC 4.1.1.22) | protein | 70 | 10% helix, 29% 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.65 | 0.78 | 52 | PYR |
| 2 | 465 | 0.62 | 0.76 | 50 | PYR |
| 3 | 368 | 0.60 | 0.76 | 40 | PYR |
| 4 | 145 | 0.55 | 0.82 | 51 | empty |
| 5 | 113 | 0.47 | 0.80 | 22 | empty |
Interfaces
15 interfaces between chains.
- E–F · 3087 Ų buried · 61 hydrogen bonds · protein-protein
- C–D · 3055 Ų buried · 65 hydrogen bonds · protein-protein
- A–B · 2989 Ų buried · 59 hydrogen bonds · protein-protein
- D–E · 610 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 542 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 1IBU · Structure of the D53,54N mutant of histidine decarboxylase at 25 C · 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 0.98
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 1IBU · PDBe 1IBU · UniProt P00862
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.