MolNFT v1 · #19307 · protein
Cystathionine gamma-synthase from nicotiana tabacum
1QGN · Protein (cystathionine gamma-synthase): “Cystathionine gamma-synthase from nicotiana tabacum”. X-ray diffraction, 1 ligand (PLP), 20 pockets (best druggability 0.83). MolNFT v1 #19307 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1QGN
- Type
- protein
- Length
- 3,184 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (cystathionine gamma-synthase)
- EC
- 4.2.99.9
- UniProt
- Q9ZPL5
- Ligands
- PLP
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Protein (cystathionine gamma-synthase) (EC 4.2.99.9) | protein | 398 | 42% helix, 16% strand | Q9ZPL5 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 8 copies · chains A, C, B, D, E, G, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.83 | 0.86 | 117 | PLP |
| 2 | 200 | 0.83 | 0.96 | 20 | empty |
| 3 | 199 | 0.83 | 0.96 | 21 | empty |
| 4 | 971 | 0.82 | 0.83 | 125 | empty |
| 5 | 642 | 0.81 | 0.85 | 98 | empty |
Interfaces
15 interfaces between chains.
- B–D · 2631 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 2630 Ų buried · 16 hydrogen bonds · protein-protein
- E–G · 2630 Ų buried · 16 hydrogen bonds · protein-protein
- F–H · 2617 Ų buried · 16 hydrogen bonds · protein-protein
- E–H · 1919 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1QGN · Cystathionine gamma-synthase from nicotiana tabacum · the same entry in another collection · chain H against H, 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 Q9ZPL5
- Elsewhere: RCSB PDB 1QGN · PDBe 1QGN · UniProt Q9ZPL5
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