Research workbench
In-flow serial synchrotron crystallography using a 3D-printed microfluidic device (3D-mixd): aspartate alpha-decarboxylase
Analyse In-flow serial synchrotron crystallography using a 3D-printed microfluidic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RXH
- Type
- protein
- Length
- 239 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate 1-decarboxylase
- EC
- 4.1.1.11
- UniProt
- A0A403CTL2, A0A3U0WEI2
- Ligands
- PYR, UNX
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate 1-decarboxylase (EC 4.1.1.11) | protein | 26 | 0% helix, 62% strand | A0A403CTL2 |
| B | Aspartate 1-decarboxylase (EC 4.1.1.11) | protein | 98 | 21% helix, 42% strand | A0A3U0WEI2 |
| D | Aspartate 1-decarboxylase (EC 4.1.1.11) | protein | 25 | 0% helix, 64% strand | A0A403CTL2 |
| E | Aspartate 1-decarboxylase (EC 4.1.1.11) | protein | 90 | 18% helix, 46% strand | A0A3U0WEI2 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 2 copies · chains B, E
- UNX · Unknown atom or ion · ion · 7 copies · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.68 | 0.96 | 15 | PYR, UNX |
| 2 | 56 | 0.28 | 0.74 | 17 | empty |
Interfaces
6 interfaces between chains.
- D–E · 1708 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 1701 Ų buried · 38 hydrogen bonds · protein-protein
- A–E · 512 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 483 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 214 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6RXH · In-flow serial synchrotron crystallography using a 3D-printed microfluidic device… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A403CTL2
- Every structure of UniProt A0A3U0WEI2
- Elsewhere: RCSB PDB 6RXH · PDBe 6RXH · UniProt A0A403CTL2 · UniProt A0A3U0WEI2
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