Research workbench
R487A mutant of L-aspartate beta-decarboxylase
Analyse R487A mutant of 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
- 2ZY5
- Type
- protein
- Length
- 3,083 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 0.77
Structure
x-ray diffraction · 5 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, C | L-aspartate beta-decarboxylase (EC 4.1.1.12) | protein | 515 | 52% helix, 12% strand | Q93QX0 |
| D | L-aspartate beta-decarboxylase (EC 4.1.1.12) | protein | 511 | 52% helix, 12% strand | Q93QX0 |
| E | L-aspartate beta-decarboxylase (EC 4.1.1.12) | protein | 511 | 52% helix, 11% strand | Q93QX0 |
| F | L-aspartate beta-decarboxylase (EC 4.1.1.12) | protein | 521 | 51% 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 | 112 | 0.77 | 0.97 | 27 | empty |
| 2 | 121 | 0.76 | 0.96 | 24 | empty |
| 3 | 509 | 0.75 | 0.83 | 62 | empty |
| 4 | 589 | 0.69 | 0.78 | 67 | empty |
| 5 | 237 | 0.69 | 0.85 | 37 | empty |
Interfaces
10 interfaces between chains.
- A–B · 3734 Ų buried · 56 hydrogen bonds · protein-protein
- C–D · 3730 Ų buried · 58 hydrogen bonds · protein-protein
- A–D · 738 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 730 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 637 Ų buried · 17 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 2ZY5 · PDBe 2ZY5 · UniProt Q93QX0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.