MolNFT v1 · #64296 · protein
Crystal structure of apo glutamate decarboxylase beta from escherichia COLI
3FZ7: “Crystal structure of apo glutamate decarboxylase beta from escherichia COLI”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.85). MolNFT v1 #64296 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3FZ7
- Type
- protein
- Length
- 2,745 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
- PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Glutamate decarboxylase beta (EC 4.1.1.15) | protein | 454 | 38% helix, 18% strand | P69910 |
| B, E | Glutamate decarboxylase beta (EC 4.1.1.15) | protein | 455 | 38% helix, 18% strand | P69910 |
| C | Glutamate decarboxylase beta (EC 4.1.1.15) | protein | 463 | 38% helix, 17% strand | P69910 |
| F | Glutamate decarboxylase beta (EC 4.1.1.15) | protein | 464 | 39% helix, 17% strand | P69910 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, F, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.85 | 0.86 | 96 | empty |
| 2 | 970 | 0.84 | 0.85 | 87 | empty |
| 3 | 924 | 0.83 | 0.85 | 76 | empty |
| 4 | 503 | 0.74 | 0.83 | 55 | empty |
| 5 | 360 | 0.72 | 0.84 | 33 | empty |
Interfaces
12 interfaces between chains.
- D–E · 5681 Ų buried · 83 hydrogen bonds · protein-protein
- A–F · 5661 Ų buried · 87 hydrogen bonds · protein-protein
- B–C · 5655 Ų buried · 85 hydrogen bonds · protein-protein
- C–D · 2596 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2312 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 3FZ7 · Crystal structure of apo glutamate decarboxylase beta from Escherichia coli · 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 B 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 3FZ7 · PDBe 3FZ7 · UniProt P69910
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