Research workbench
Conformational dynamics of aspartate alpha-decarboxylase active site revealed by protein-ligand complexes: 1-methyl- L-aspartate complex
Analyse Conformational dynamics of aspartate alpha-decarboxylase active site revealed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AOK
- Type
- protein
- Length
- 243 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate 1-decarboxylase beta chain; Aspartate 1-decarboxylase alpha chain
- EC
- 4.1.1.11
- UniProt
- P0A790
- Pockets
- 1 · best druggability 0.30
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate 1-decarboxylase beta chain (EC 4.1.1.11) | protein | 27 | 0% helix, 59% strand | P0A790 |
| B | Aspartate 1-decarboxylase alpha chain (EC 4.1.1.11) | protein | 99 | 21% helix, 43% strand | P0A790 |
| D | Aspartate 1-decarboxylase beta chain (EC 4.1.1.11) | protein | 25 | 0% helix, 64% strand | P0A790 |
| E | Aspartate 1-decarboxylase alpha chain (EC 4.1.1.11) | protein | 92 | 17% helix, 47% strand | P0A790 |
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 | 67 | 0.30 | 0.74 | 20 | empty |
Interfaces
6 interfaces between chains.
- D–E · 1699 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 1689 Ų buried · 39 hydrogen bonds · protein-protein
- A–E · 549 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 515 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 210 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 4AOK · Conformational dynamics of aspartate alpha-decarboxylase active site revealed by… · the same entry in another collection · chain E against E, TM-score 1.00
- P0A790 · AlphaFold monomer V2.0 prediction for aspartate 1-decarboxylase (P0A790) · a predicted model of the same protein · chain E 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 4AOK · PDBe 4AOK · UniProt P0A790
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