MolNFT v1 · #116716 · protein
Crystal structure of glutamine synthetase from chromohalobacter salexigens dsm 3043(CSAL_0679, target efi-550015) with bound ADP
5DM3 · L-glutamine synthetase: “Crystal structure of glutamine synthetase from chromohalobacter salexigens dsm 3043(CSAL_0679, target…”. X-ray diffraction, 1 ligand (ADP), 20 pockets (best druggability 0.73). MolNFT v1 #116716 on…
- PDB
- 5DM3
- Type
- protein
- Length
- 2,305 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-glutamine synthetase
- EC
- 6.3.1.2
- UniProt
- Q1QZR8
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-glutamine synthetase (EC 6.3.1.2) | protein | 374 | 40% helix, 23% strand | Q1QZR8 |
| B | L-glutamine synthetase (EC 6.3.1.2) | protein | 385 | 39% helix, 25% strand | Q1QZR8 |
| C | L-glutamine synthetase (EC 6.3.1.2) | protein | 396 | 39% helix, 22% strand | Q1QZR8 |
| D | L-glutamine synthetase (EC 6.3.1.2) | protein | 386 | 38% helix, 24% strand | Q1QZR8 |
| E | L-glutamine synthetase (EC 6.3.1.2) | protein | 383 | 40% helix, 24% strand | Q1QZR8 |
| F | L-glutamine synthetase (EC 6.3.1.2) | protein | 381 | 41% helix, 23% strand | Q1QZR8 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, D, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 884 | 0.73 | 0.77 | 79 | ADP |
| 2 | 528 | 0.68 | 0.79 | 60 | ADP |
| 3 | 657 | 0.67 | 0.76 | 58 | empty |
| 4 | 676 | 0.65 | 0.75 | 53 | ADP |
| 5 | 504 | 0.65 | 0.77 | 46 | ADP |
Interfaces
6 interfaces between chains.
- B–C · 873 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 863 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 805 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 801 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 773 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5DM3 · Crystal Structure of Glutamine Synthetase from Chromohalobacter salexigens DSM… · the same entry in another collection · 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 Q1QZR8
- Elsewhere: RCSB PDB 5DM3 · PDBe 5DM3 · UniProt Q1QZR8
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