Research workbench
Dodecameric L-aspartate beta-decarboxylase
Analyse Dodecameric L-aspartate beta-decarboxylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZY4
- Type
- protein
- Length
- 3,106 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-aspartate beta-decarboxylase
- EC
- 4.1.1.12
- UniProt
- Q93QX0
- Ligands
- PLP, CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-aspartate beta-decarboxylase (EC 4.1.1.12) | protein | 524 | 53% helix, 13% strand | Q93QX0 |
| B | L-aspartate beta-decarboxylase (EC 4.1.1.12) | protein | 512 | 53% helix, 13% strand | Q93QX0 |
| C | L-aspartate beta-decarboxylase (EC 4.1.1.12) | protein | 511 | 52% helix, 13% strand | Q93QX0 |
| D | L-aspartate beta-decarboxylase (EC 4.1.1.12) | protein | 515 | 54% helix, 12% strand | Q93QX0 |
| E | L-aspartate beta-decarboxylase (EC 4.1.1.12) | protein | 509 | 52% helix, 11% strand | Q93QX0 |
| F | L-aspartate beta-decarboxylase (EC 4.1.1.12) | protein | 535 | 54% helix, 11% strand | Q93QX0 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.78 | 0.97 | 26 | empty |
| 2 | 908 | 0.77 | 0.80 | 89 | CL |
| 3 | 119 | 0.77 | 0.96 | 26 | empty |
| 4 | 558 | 0.67 | 0.77 | 66 | empty |
| 5 | 506 | 0.67 | 0.78 | 68 | empty |
Interfaces
9 interfaces between chains.
- A–B · 3837 Ų buried · 53 hydrogen bonds · protein-protein
- C–D · 3653 Ų buried · 53 hydrogen bonds · protein-protein
- A–D · 783 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 729 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 646 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (pyridoxal phosphate Schiff base).
Compared structures
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 Q93QX0
- Elsewhere: RCSB PDB 2ZY4 · PDBe 2ZY4 · UniProt Q93QX0
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