Research workbench
Crystal structure of glutamate decarboxylase domain of diaminobutyrate-pyruvate transaminase and L-2,4-diaminobutyrate decarboxylase from vibrio parahaemolyticus
Analyse Crystal structure of glutamate decarboxylase domain of diaminobutyrate-pyruvate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QMA
- Type
- protein
- Length
- 922 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminobutyrate-pyruvate transaminase and L-2,4- diaminobutyrate decarboxylase
- UniProt
- Q87NC6
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diaminobutyrate-pyruvate transaminase and L-2,4- diaminobutyrate decarboxylase | protein | 463 | 50% helix, 15% strand | Q87NC6 |
| B | Diaminobutyrate-pyruvate transaminase and L-2,4- diaminobutyrate decarboxylase | protein | 459 | 50% helix, 15% strand | Q87NC6 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.78 | 0.80 | 93 | empty |
| 2 | 59 | 0.72 | 0.98 | 20 | empty |
| 3 | 244 | 0.58 | 0.79 | 35 | empty |
| 4 | 107 | 0.46 | 0.79 | 21 | empty |
| 5 | 54 | 0.26 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 6584 Ų buried · 87 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 modified (engineered).
Compared structures
- 2QMA · Crystal structure of glutamate decarboxylase domain of diaminobutyrate-pyruvate… · 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 Q87NC6
- Elsewhere: RCSB PDB 2QMA · PDBe 2QMA · UniProt Q87NC6
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