MolNFT v1 · #120098 · protein
Lactobacillus brevis cgmcc 1306 glutamate decarboxylase
5GP4: “Lactobacillus brevis cgmcc 1306 glutamate decarboxylase”. X-ray diffraction, 1 ligand (PLP), 12 pockets (best druggability 0.83). MolNFT v1 #120098 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GP4
- Type
- protein
- Length
- 1,304 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate decarboxylase
- EC
- 4.1.1.15
- UniProt
- D6PXK5
- Ligands
- PLP
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Glutamate decarboxylase (EC 4.1.1.15) | protein | 439 | 40% helix, 17% strand | D6PXK5 |
| A | Glutamate decarboxylase (EC 4.1.1.15) | protein | 441 | 40% helix, 16% strand | D6PXK5 |
| B | Glutamate decarboxylase (EC 4.1.1.15) | protein | 424 | 40% helix, 17% strand | D6PXK5 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.83 | 0.85 | 102 | empty |
| 2 | 747 | 0.75 | 0.80 | 71 | empty |
| 3 | 360 | 0.67 | 0.80 | 36 | empty |
| 4 | 122 | 0.63 | 0.87 | 18 | empty |
| 5 | 286 | 0.56 | 0.76 | 26 | empty |
Interfaces
3 interfaces between chains.
- C–A · 4767 Ų buried · 68 hydrogen bonds · protein-protein
- A–B · 1886 Ų buried · 31 hydrogen bonds · protein-protein
- C–B · 208 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5GP4 · Lactobacillus brevis CGMCC 1306 Glutamate decarboxylase · the same entry in another collection · chain C against C, 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 D6PXK5
- Elsewhere: RCSB PDB 5GP4 · PDBe 5GP4 · UniProt D6PXK5
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