MolNFT v1 · #57029 · protein
Dodecameric L-aspartate beta-decarboxylase
2ZY3: “Dodecameric L-aspartate beta-decarboxylase”. X-ray diffraction, 1 ligand (PLP), 20 pockets (best druggability 0.81). MolNFT v1 #57029 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2ZY3
- Type
- protein
- Length
- 3,090 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
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-aspartate beta-decarboxylase (EC 4.1.1.12) | protein | 510 | 51% helix, 12% strand | Q93QX0 |
| B | L-aspartate beta-decarboxylase (EC 4.1.1.12) | protein | 515 | 53% helix, 12% strand | Q93QX0 |
| C | L-aspartate beta-decarboxylase (EC 4.1.1.12) | protein | 516 | 53% helix, 12% strand | Q93QX0 |
| D | L-aspartate beta-decarboxylase (EC 4.1.1.12) | protein | 514 | 52% helix, 12% strand | Q93QX0 |
| E | L-aspartate beta-decarboxylase (EC 4.1.1.12) | protein | 512 | 52% helix, 11% strand | Q93QX0 |
| F | L-aspartate beta-decarboxylase (EC 4.1.1.12) | protein | 523 | 53% helix, 11% strand | Q93QX0 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 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 | 995 | 0.81 | 0.82 | 104 | empty |
| 2 | 123 | 0.77 | 0.97 | 25 | empty |
| 3 | 124 | 0.76 | 0.95 | 24 | empty |
| 4 | 54 | 0.72 | 0.99 | 22 | PLP |
| 5 | 750 | 0.68 | 0.75 | 51 | empty |
Interfaces
10 interfaces between chains.
- A–B · 3717 Ų buried · 56 hydrogen bonds · protein-protein
- C–D · 3703 Ų buried · 51 hydrogen bonds · protein-protein
- A–D · 770 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 743 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 673 Ų buried · 9 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 2ZY3 · PDBe 2ZY3 · UniProt Q93QX0
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