Research workbench
Gk domain of drosophila P5CS filament with glutamate, ATP, and NADPH
Analyse Gk domain of drosophila P5CS filament with glutamate, ATP, and NADPH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WX3
- Type
- protein
- Length
- 1,082 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Delta-1-pyrroline-5-carboxylate synthase
- EC
- 2.7.2.11, 1.2.1.41
- UniProt
- Q9VNW6
- Ligands
- RGP, ADP, MG
- Pockets
- 13 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Delta-1-pyrroline-5-carboxylate synthase (EC 2.7.2.11, 1.2.1.41) | protein | 252 | 41% helix, 17% strand | Q9VNW6 |
| E, F, G, H | Delta-1-pyrroline-5-carboxylate synthase (EC 2.7.2.11, 1.2.1.41) | protein | 14 | 29% helix, 7% strand | Q9VNW6 |
| B, C, D | Delta-1-pyrroline-5-carboxylate synthase (EC 2.7.2.11, 1.2.1.41) | protein | 258 | 42% helix, 17% strand | Q9VNW6 |
Ligands and binding sites
- RGP · Gamma-glutamyl phosphate · ligand · 4 copies · chains A, B, C, D
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.86 | 0.86 | 118 | empty |
| 2 | 143 | 0.62 | 0.86 | 37 | empty |
| 3 | 141 | 0.57 | 0.83 | 33 | empty |
| 4 | 82 | 0.41 | 0.79 | 19 | empty |
| 5 | 85 | 0.39 | 0.77 | 19 | empty |
Interfaces
20 interfaces between chains.
- A–D · 1616 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1613 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 836 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 836 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 455 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7WX3 · GK domain of Drosophila P5CS filament with glutamate, ATP, and NADPH · 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 Q9VNW6
- Elsewhere: RCSB PDB 7WX3 · PDBe 7WX3 · UniProt Q9VNW6
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