Research workbench
Structural insight into the substrate inhibition mechanism of NADP+- dependent succinic semialdehyde dehydrogenase from streptococcus pyogenes
Analyse Structural insight into the substrate inhibition mechanism of NADP+- dependent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YWV
- Type
- protein
- Length
- 910 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinic semialdehyde dehydrogenase
- EC
- 1.2.1.79
- Ligands
- SSN, SO4
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Succinic semialdehyde dehydrogenase (EC 1.2.1.79) | protein | 455 | 45% helix, 20% strand | — |
Ligands and binding sites
- SSN · 4-oxobutanoic acid · ligand · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.83 | 0.84 | 129 | empty |
| 2 | 385 | 0.62 | 0.77 | 37 | SSN |
| 3 | 350 | 0.61 | 0.78 | 38 | SSN |
| 4 | 141 | 0.48 | 0.78 | 20 | empty |
| 5 | 98 | 0.39 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2562 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 4YWV · Structural insight into the substrate inhibition mechanism of NADP+-dependent succinic… · 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
- Elsewhere: RCSB PDB 4YWV · PDBe 4YWV
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