Research workbench
Crystal structure of human glutamine synthetase in complex with ADP and phosphate
Analyse Crystal structure of human glutamine synthetase in complex with ADP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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