MolNFT v1 · #40972 · protein
Structure of GLNK1 with bound effectors indicates regulatory mechanism for ammonia uptake
2J9E · Hypothetical nitrogen regulatory pii-like protein MJ0059: “Structure of GLNK1 with bound effectors indicates regulatory mechanism for ammonia uptake”. X-ray diffraction, 5 ligands (ATP, AKG, NA), 3 pockets (best druggability 0.76).…
- PDB
- 2J9E
- Type
- protein
- Length
- 347 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical nitrogen regulatory pii-like protein MJ0059
- UniProt
- Q60381
- Ligands
- ATP, AKG, NA, MG, CL
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical nitrogen regulatory pii-like protein MJ0059 | protein | 112 | 29% helix, 39% strand | Q60381 |
| B | Hypothetical nitrogen regulatory pii-like protein MJ0059 | protein | 119 | 28% helix, 40% strand | Q60381 |
| C | Hypothetical nitrogen regulatory pii-like protein MJ0059 | protein | 116 | 27% helix, 39% strand | Q60381 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, C, B
- AKG · 2-oxoglutaric acid · ligand · chains C
- NA · Sodium ion · metal · chains B, C
- MG · Magnesium ion · metal · chains C
- CL · Chloride ion · ion · 4 copies · chains A, B, C
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 368 | 0.76 | 0.86 | 50 | ATP, MG |
| 2 | 284 | 0.75 | 0.87 | 41 | ATP |
| 3 | 295 | 0.71 | 0.85 | 40 | ATP |
Interfaces
3 interfaces between chains.
- B–C · 1448 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1309 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 1240 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2J9E · Structure of GlnK1 with bound effectors indicates regulatory mechanism for ammonia uptake · the same entry in another collection · chain A against A, TM-score 1.00
- Q60381 · AlphaFold monomer V2.0 prediction for uncharacterized nitrogen regulatory pii-like… · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q60381
- Elsewhere: RCSB PDB 2J9E · PDBe 2J9E · UniProt Q60381
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