MolNFT v1 · #40854 · protein
Glutamate 5-kinase from escherichia COLI complexed with glutamate
2J5T: “Glutamate 5-kinase from escherichia COLI complexed with glutamate”. X-ray diffraction, 4 ligands (GLU, MG, CL), 20 pockets (best druggability 0.71). MolNFT v1 #40854 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2J5T
- Type
- protein
- Length
- 2,841 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate 5-kinase
- EC
- 2.7.2.11
- UniProt
- P0A7B5
- Ligands
- GLU, MG, CL, SO4
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate 5-kinase (EC 2.7.2.11) | protein | 355 | 40% helix, 21% strand | P0A7B5 |
| B | Glutamate 5-kinase (EC 2.7.2.11) | protein | 353 | 41% helix, 21% strand | P0A7B5 |
| C, G | Glutamate 5-kinase (EC 2.7.2.11) | protein | 356 | 42% helix, 19% strand | P0A7B5 |
| D, E | Glutamate 5-kinase (EC 2.7.2.11) | protein | 365 | 41% helix, 20% strand | P0A7B5 |
| F | Glutamate 5-kinase (EC 2.7.2.11) | protein | 354 | 40% helix, 21% strand | P0A7B5 |
| H | Glutamate 5-kinase (EC 2.7.2.11) | protein | 337 | 41% helix, 22% strand | P0A7B5 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 12 copies · chains A, B, C, D, E, F, G
- MG · Magnesium ion · metal · 8 copies · chains A, B, D, E, F, G, H
- CL · Chloride ion · ion · 20 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.71 | 0.76 | 59 | CL |
| 2 | 909 | 0.70 | 0.76 | 62 | empty |
| 3 | 919 | 0.69 | 0.75 | 78 | GLU, SO4 |
| 4 | 495 | 0.64 | 0.76 | 48 | MG |
| 5 | 514 | 0.63 | 0.76 | 52 | MG |
Interfaces
11 interfaces between chains.
- E–F · 2254 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2244 Ų buried · 38 hydrogen bonds · protein-protein
- G–H · 2238 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2201 Ų buried · 36 hydrogen bonds · protein-protein
- E–G · 457 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
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 2J5T · PDBe 2J5T · UniProt P0A7B5
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