MolNFT v1 · #64297 · protein
Crystal structure of glutamate decarboxylase beta from escherichia COLI: reduced schiff base with plp
3FZ8: “Crystal structure of glutamate decarboxylase beta from escherichia COLI: reduced schiff base with plp”. X-ray diffraction, 1 ligand (PLR), 20 pockets (best druggability 0.83). MolNFT v1 #64297 on GenesisL1: 3D structure, binding…
- PDB
- 3FZ8
- Type
- protein
- Length
- 2,747 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate decarboxylase beta
- EC
- 4.1.1.15
- UniProt
- P69910
- Ligands
- PLR
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F | Glutamate decarboxylase beta (EC 4.1.1.15) | protein | 455 | 38% helix, 17% strand | P69910 |
| B | Glutamate decarboxylase beta (EC 4.1.1.15) | protein | 463 | 38% helix, 16% strand | P69910 |
| E | Glutamate decarboxylase beta (EC 4.1.1.15) | protein | 464 | 38% helix, 17% strand | P69910 |
Ligands and binding sites
- PLR · (5-hydroxy-4,6-dimethylpyridin-3-yl)methyl dihydrogen 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 | 935 | 0.83 | 0.85 | 80 | empty |
| 2 | 720 | 0.82 | 0.86 | 68 | empty |
| 3 | 611 | 0.82 | 0.87 | 67 | empty |
| 4 | 400 | 0.73 | 0.83 | 36 | empty |
| 5 | 53 | 0.71 | 0.99 | 23 | PLR |
Interfaces
12 interfaces between chains.
- E–F · 5763 Ų buried · 75 hydrogen bonds · protein-protein
- A–B · 5758 Ų buried · 74 hydrogen bonds · protein-protein
- C–D · 5737 Ų buried · 73 hydrogen bonds · protein-protein
- B–C · 2652 Ų buried · 38 hydrogen bonds · protein-protein
- A–F · 2335 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 3FZ8 · Crystal structure of glutamate decarboxylase beta from Escherichia coli: reduced Schiff… · the same entry in another collection · chain F against F, TM-score 1.00
- P69910 · AlphaFold monomer V2.0 prediction for glutamate decarboxylase beta (P69910) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P69910
- Elsewhere: RCSB PDB 3FZ8 · PDBe 3FZ8 · UniProt P69910
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