Research workbench
Cystathionine gamma-synthase in complex with the inhibitor appa
Analyse Cystathionine gamma-synthase in complex with the inhibitor appa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1I41
- Type
- protein
- Length
- 4,752 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine gamma-synthase
- EC
- 4.2.99.9
- UniProt
- Q9ZPL5
- Ligands
- HEN
- Pockets
- 20 · best druggability 0.85
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, I, J, K, L | Cystathionine gamma-synthase (EC 4.2.99.9) | protein | 396 | 42% helix, 16% strand | Q9ZPL5 |
Ligands and binding sites
- HEN · 2-[(3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl)-imino]-5-phosphono-pent-3-enoic acid · ligand · 12 copies · chains A, C, B, D, E, G, F, H, I, K, J, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.85 | 0.86 | 150 | HEN |
| 2 | 191 | 0.82 | 0.96 | 22 | empty |
| 3 | 523 | 0.82 | 0.88 | 85 | HEN |
| 4 | 503 | 0.81 | 0.88 | 92 | HEN |
| 5 | 551 | 0.81 | 0.87 | 90 | HEN |
Interfaces
18 interfaces between chains.
- F–H · 2677 Ų buried · 24 hydrogen bonds · protein-protein
- E–G · 2672 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 2667 Ų buried · 23 hydrogen bonds · protein-protein
- I–K · 2662 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 2640 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1I41 · Cystathionine gamma-synthase in complex with the inhibitor appa · 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 Q9ZPL5
- Elsewhere: RCSB PDB 1I41 · PDBe 1I41 · UniProt Q9ZPL5
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