MolNFT v1 · #46947 · protein
Crystal structure of human glutamine synthetase in complex with ADP and phosphate
2OJW: “Crystal structure of human glutamine synthetase in complex with ADP and phosphate”. X-ray diffraction, 4 ligands (ADP, MN, PO4), 17 pockets (best druggability 0.80). MolNFT v1 #46947 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2OJW
- Type
- protein
- Length
- 1,802 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamine synthetase
- EC
- 6.3.1.2
- UniProt
- P15104
- Ligands
- ADP, MN, PO4, CL
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamine synthetase (EC 6.3.1.2) | protein | 360 | 30% helix, 25% strand | P15104 |
| B | Glutamine synthetase (EC 6.3.1.2) | protein | 362 | 31% helix, 24% strand | P15104 |
| C | Glutamine synthetase (EC 6.3.1.2) | protein | 364 | 30% helix, 25% strand | P15104 |
| D | Glutamine synthetase (EC 6.3.1.2) | protein | 362 | 30% helix, 25% strand | P15104 |
| E | Glutamine synthetase (EC 6.3.1.2) | protein | 354 | 30% helix, 25% strand | P15104 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, E, B, C, D
- MN · Manganese (II) ion · metal · 20 copies · chains A, B, C, D, E
- PO4 · Phosphate ion · ion · 5 copies · chains A, E, B, C, D
- CL · Chloride ion · ion · 5 copies · chains A, E, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 884 | 0.80 | 0.83 | 102 | GOL |
| 2 | 761 | 0.75 | 0.80 | 83 | MN, PO4, ADP |
| 3 | 783 | 0.75 | 0.80 | 84 | MN, PO4, ADP |
| 4 | 675 | 0.74 | 0.81 | 76 | MN, PO4, ADP |
| 5 | 714 | 0.74 | 0.80 | 77 | MN, PO4, ADP |
Interfaces
5 interfaces between chains.
- D–E · 2456 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2444 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 2438 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2394 Ų buried · 41 hydrogen bonds · protein-protein
- A–E · 2247 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 2OJW · Crystal structure of human glutamine synthetase in complex with ADP and phosphate · the same entry in another collection · chain E against E, TM-score 1.00
- P15104 · AlphaFold monomer V2.0 prediction for glutamine synthetase (P15104) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 P15104
- Elsewhere: RCSB PDB 2OJW · PDBe 2OJW · UniProt P15104
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