Research workbench
Glutamate 5-kinase from escherichia COLI complexed with glutamyl-5-phosphate and pyroglutamic acid
Analyse Glutamate 5-kinase from escherichia COLI complexed with glutamyl-5-phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J5V
- Type
- protein
- Length
- 648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate 5-kinase
- EC
- 2.7.2.11
- UniProt
- P0A7B5
- Ligands
- PCA, RGP, MG, SO4
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate 5-kinase (EC 2.7.2.11) | protein | 323 | 45% helix, 20% strand | P0A7B5 |
| B | Glutamate 5-kinase (EC 2.7.2.11) | protein | 325 | 43% helix, 22% strand | P0A7B5 |
Ligands and binding sites
- PCA · Pyroglutamic acid · ligand · 2 copies · chains A, B
- RGP · Gamma-glutamyl phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.60 | 0.76 | 39 | empty |
| 2 | 205 | 0.53 | 0.77 | 24 | empty |
| 3 | 173 | 0.50 | 0.77 | 20 | empty |
| 4 | 152 | 0.42 | 0.74 | 33 | MG, PCA, RGP, SO4 |
| 5 | 134 | 0.41 | 0.75 | 27 | PCA, RGP, SO4 |
Interfaces
1 interface between chains.
- A–B · 2291 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 2J5V · Glutamate 5-kinase from escherichia COLI complexed with glutamyl-5-phosphate and… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A7B5 · AlphaFold monomer V2.0 prediction for glutamate 5-kinase (P0A7B5) · a predicted model of the same protein · chain A 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 P0A7B5
- Elsewhere: RCSB PDB 2J5V · PDBe 2J5V · UniProt P0A7B5
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