Research workbench
Crystal structure of escherichia COLI gadb in complex with bromide
Analyse Crystal structure of escherichia COLI gadb in complex with bromide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DGL
- Type
- protein
- Length
- 2,704 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
- PLP, BR
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Glutamate decarboxylase beta (EC 4.1.1.15) | protein | 450 | 42% helix, 17% strand | P69910 |
| C, F | Glutamate decarboxylase beta (EC 4.1.1.15) | protein | 451 | 41% helix, 17% strand | P69910 |
| E | Glutamate decarboxylase beta (EC 4.1.1.15) | protein | 452 | 42% helix, 16% strand | P69910 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- BR · Bromide ion · ion · 24 copies · chains A, F, B, C, D, E
- ACY · Acetic acid · additive · 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 | 768 | 0.80 | 0.84 | 70 | BR |
| 2 | 610 | 0.79 | 0.85 | 67 | BR |
| 3 | 604 | 0.78 | 0.84 | 65 | BR |
| 4 | 633 | 0.78 | 0.84 | 69 | BR |
| 5 | 599 | 0.78 | 0.84 | 69 | BR |
Interfaces
12 interfaces between chains.
- C–D · 4847 Ų buried · 76 hydrogen bonds · protein-protein
- E–F · 4837 Ų buried · 74 hydrogen bonds · protein-protein
- A–B · 4800 Ų buried · 71 hydrogen bonds · protein-protein
- B–C · 2164 Ų buried · 40 hydrogen bonds · protein-protein
- D–E · 2150 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2DGL · Crystal structure of Escherichia coli GadB in complex with bromide · 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 D 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 P69910
- Elsewhere: RCSB PDB 2DGL · PDBe 2DGL · UniProt P69910
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