Research workbench
Structure determination of cystathionine gamma-synthase from helicobacter pylori
Analyse Structure determination of cystathionine gamma-synthase 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
- 4L0O
- Type
- protein
- Length
- 2,941 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine gamma-synthase
- EC
- 2.5.1.48
- UniProt
- P56069
- Ligands
- PLP, PO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 8 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Cystathionine gamma-synthase (EC 2.5.1.48) | protein | 373 | 38% helix, 16% strand | P56069 |
| A | Cystathionine gamma-synthase (EC 2.5.1.48) | protein | 363 | 37% helix, 17% strand | P56069 |
| C | Cystathionine gamma-synthase (EC 2.5.1.48) | protein | 366 | 39% helix, 17% strand | P56069 |
| E | Cystathionine gamma-synthase (EC 2.5.1.48) | protein | 364 | 37% helix, 16% strand | P56069 |
| G | Cystathionine gamma-synthase (EC 2.5.1.48) | protein | 365 | 40% helix, 17% strand | P56069 |
| K | Cystathionine gamma-synthase (EC 2.5.1.48) | protein | 378 | 40% helix, 17% strand | P56069 |
| M | Cystathionine gamma-synthase (EC 2.5.1.48) | protein | 365 | 35% helix, 17% strand | P56069 |
| O | Cystathionine gamma-synthase (EC 2.5.1.48) | protein | 367 | 38% helix, 16% strand | P56069 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 7 copies · chains H, E, A, C, G, M, O
- PO4 · Phosphate ion · ion · chains K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 857 | 0.80 | 0.83 | 103 | PLP |
| 2 | 72 | 0.74 | 0.98 | 33 | empty |
| 3 | 54 | 0.72 | 0.99 | 31 | empty |
| 4 | 830 | 0.72 | 0.77 | 95 | PLP |
| 5 | 56 | 0.72 | 0.99 | 32 | empty |
Interfaces
11 interfaces between chains.
- A–C · 2609 Ų buried · 32 hydrogen bonds · protein-protein
- M–O · 2583 Ų buried · 30 hydrogen bonds · protein-protein
- H–E · 2233 Ų buried · 22 hydrogen bonds · protein-protein
- H–G · 478 Ų buried · 3 hydrogen bonds · protein-protein
- E–G · 400 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4L0O · Structure determination of cystathionine gamma-synthase from Helicobacter pylori · the same entry in another collection · chain C against C, TM-score 1.00
- P56069 · AlphaFold monomer V2.0 prediction for cystathionine gamma-synthase (P56069) · a predicted model of the same protein · chain C 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 P56069
- Elsewhere: RCSB PDB 4L0O · PDBe 4L0O · UniProt P56069
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.