MolNFT v1 · #34449 · protein
Crystal structure of escherichia COLI gadb in complex with iodide
2DGM · Glutamate decarboxylase beta: “Crystal structure of escherichia COLI gadb in complex with iodide”. X-ray diffraction, 2 ligands (PLP, IOD), 20 pockets (best druggability 0.84). MolNFT v1 #34449 on GenesisL1: 3D structure, binding…
- PDB
- 2DGM
- Type
- protein
- Length
- 2,715 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, IOD
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate decarboxylase beta (EC 4.1.1.15) | protein | 452 | 43% helix, 17% strand | P69910 |
| B | Glutamate decarboxylase beta (EC 4.1.1.15) | protein | 451 | 42% helix, 17% strand | P69910 |
| C, D, F | Glutamate decarboxylase beta (EC 4.1.1.15) | protein | 454 | 43% helix, 17% strand | P69910 |
| E | Glutamate decarboxylase beta (EC 4.1.1.15) | protein | 450 | 43% helix, 17% strand | P69910 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- IOD · Iodide ion · ion · 32 copies · chains A, F, B, C, D, E
- FMT · Formic acid · additive · 13 copies · chains A, B, C, D, E, F
- ACY · Acetic acid · additive · chains E, F
- PEG · Di(hydroxyethyl)ether · additive · chains 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.84 | 0.85 | 122 | IOD, PLP, FMT |
| 2 | 977 | 0.83 | 0.85 | 112 | IOD, ACY, FMT |
| 3 | 1028 | 0.83 | 0.84 | 107 | IOD, FMT |
| 4 | 803 | 0.79 | 0.83 | 78 | IOD |
| 5 | 596 | 0.79 | 0.85 | 67 | IOD |
Interfaces
12 interfaces between chains.
- C–D · 4812 Ų buried · 75 hydrogen bonds · protein-protein
- E–F · 4783 Ų buried · 77 hydrogen bonds · protein-protein
- A–B · 4774 Ų buried · 70 hydrogen bonds · protein-protein
- A–F · 2221 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 2215 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2DGM · Crystal structure of Escherichia coli GadB in complex with iodide · 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 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 2DGM · PDBe 2DGM · UniProt P69910
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