Research workbench
Crystal structure of glutamine synthetase from helicobacter pylori
Analyse Crystal structure of glutamine synthetase from helicobacter pylori in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZLP
- Type
- protein
- Length
- 5,704 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamine synthetase
- EC
- 6.3.1.2
- UniProt
- P94845
- Ligands
- ATP, ADP, PPQ, P3P, MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, L, G | Glutamine synthetase (EC 6.3.1.2) | protein | 476 | 34% helix, 23% strand | P94845 |
| B, F, H, K, I | Glutamine synthetase (EC 6.3.1.2) | protein | 475 | 34% helix, 24% strand | P94845 |
| C | Glutamine synthetase (EC 6.3.1.2) | protein | 474 | 35% helix, 23% strand | P94845 |
| E | Glutamine synthetase (EC 6.3.1.2) | protein | 473 | 34% helix, 23% strand | P94845 |
| J | Glutamine synthetase (EC 6.3.1.2) | protein | 478 | 35% helix, 24% strand | P94845 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains A, F, B, C, E, J, K, L, G
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains D, E, H, J, I, L
- PPQ · Phosphinothricin · ligand · 3 copies · chains J, I, K, H
- P3P · (2S)-2-amino-4-[methyl(phosphonooxy)phosphoryl]butanoic acid · ligand · chains K, L
- MG · Magnesium ion · metal · 4 copies · chains J, L, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.79 | 0.85 | 64 | empty |
| 2 | 798 | 0.78 | 0.82 | 80 | empty |
| 3 | 801 | 0.77 | 0.81 | 84 | empty |
| 4 | 634 | 0.77 | 0.83 | 64 | ADP |
| 5 | 1107 | 0.77 | 0.79 | 100 | empty |
Interfaces
24 interfaces between chains.
- E–I · 3003 Ų buried · 43 hydrogen bonds · protein-protein
- F–H · 2984 Ų buried · 42 hydrogen bonds · protein-protein
- C–K · 2984 Ų buried · 40 hydrogen bonds · protein-protein
- A–G · 2982 Ų buried · 34 hydrogen bonds · protein-protein
- B–L · 2974 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 5ZLP · Crystal structure of glutamine synthetase from helicobacter pylori · the same entry in another collection · chain K against K, 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 P94845
- Elsewhere: RCSB PDB 5ZLP · PDBe 5ZLP · UniProt P94845
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