Research workbench
Crystal structure of glutamate decarboxylase beta from escherichia COLI: complex with xenon
Analyse Crystal structure of glutamate decarboxylase beta from escherichia COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FZ6
- 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
- PMP, XE
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 39% 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 | 39% helix, 17% strand | P69910 |
| E | Glutamate decarboxylase beta (EC 4.1.1.15) | protein | 464 | 40% helix, 17% strand | P69910 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- XE · Xenon · ion · 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 | 770 | 0.83 | 0.86 | 78 | empty |
| 2 | 707 | 0.82 | 0.86 | 76 | empty |
| 3 | 623 | 0.82 | 0.87 | 74 | empty |
| 4 | 613 | 0.75 | 0.82 | 78 | empty |
| 5 | 63 | 0.73 | 0.98 | 23 | PMP |
Interfaces
12 interfaces between chains.
- C–D · 5737 Ų buried · 71 hydrogen bonds · protein-protein
- A–B · 5725 Ų buried · 77 hydrogen bonds · protein-protein
- E–F · 5687 Ų buried · 71 hydrogen bonds · protein-protein
- B–C · 2633 Ų buried · 39 hydrogen bonds · protein-protein
- A–F · 2343 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 3FZ6 · Crystal structure of glutamate decarboxylase beta from Escherichia coli: complex with… · 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 3FZ6 · PDBe 3FZ6 · UniProt P69910
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