MolNFT v1 · #18750 · protein
Processed aspartate decarboxylase mutant with SER25 mutated to cys
1PYU · Aspartate 1-decarboxylase beta chain: “Processed aspartate decarboxylase mutant with SER25 mutated to cys”. X-ray diffraction, 1 ligand (SO4), 1 pocket (best druggability 0.27). MolNFT v1 #18750 on GenesisL1: 3D structure, binding…
- PDB
- 1PYU
- Type
- protein
- Length
- 235 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate 1-decarboxylase beta chain; Aspartate 1-decarboxylase alfa chain
- EC
- 4.1.1.11
- UniProt
- P0A790
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.27
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate 1-decarboxylase beta chain (EC 4.1.1.11) | protein | 28 | 0% helix, 57% strand | P0A790 |
| B | Aspartate 1-decarboxylase alfa chain (EC 4.1.1.11) | protein | 92 | 20% helix, 46% strand | P0A790 |
| C | Aspartate 1-decarboxylase beta chain (EC 4.1.1.11) | protein | 24 | 0% helix, 67% strand | P0A790 |
| D | Aspartate 1-decarboxylase alfa chain (EC 4.1.1.11) | protein | 91 | 18% helix, 47% strand | P0A790 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.27 | 0.74 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1648 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1629 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 517 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 499 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 204 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1PYU · Processed Aspartate Decarboxylase Mutant with Ser25 mutated to Cys · the same entry in another collection · chain C against C, TM-score 1.00
- P0A790 · AlphaFold monomer V2.0 prediction for aspartate 1-decarboxylase (P0A790) · 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 P0A790
- Elsewhere: RCSB PDB 1PYU · PDBe 1PYU · UniProt P0A790
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