MolNFT v1 · #9943 · protein
Structure of the D53,54N mutant of histidine decarboxylase bound with histidine methyl ester at-170 C
1IBV · Histidine decarboxylase beta chain: “Structure of the D53,54N mutant of histidine decarboxylase bound with histidine methyl ester at-170 C”. X-ray diffraction, 2 ligands (PYR, PVH), 15 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 1IBV
- 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
- 15 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 33% 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 | 28% helix, 35% 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
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.74 | 0.99 | 18 | empty |
| 2 | 65 | 0.70 | 0.96 | 18 | PYR, PVH |
| 3 | 68 | 0.69 | 0.95 | 17 | PYR, PVH |
| 4 | 61 | 0.68 | 0.96 | 18 | PYR, PVH |
| 5 | 584 | 0.61 | 0.73 | 60 | empty |
Interfaces
15 interfaces between chains.
- A–B · 3239 Ų buried · 70 hydrogen bonds · protein-protein
- C–D · 3229 Ų buried · 68 hydrogen bonds · protein-protein
- E–F · 3218 Ų buried · 68 hydrogen bonds · protein-protein
- D–E · 947 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 944 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 1IBV · Structure of the D53,54N mutant of histidine decarboxylase bound with histidine methyl… · 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 0.99
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 1IBV · PDBe 1IBV · UniProt P00862
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