MolNFT v1 · #111643 · protein
Structural insight into the substrate inhibition mechanism of NADP+- dependent succinic semialdehyde dehydrogenase from streptococcus pyogenes
4YWU: “Structural insight into the substrate inhibition mechanism of NADP+- dependent succinic semialdehyde…”. X-ray diffraction, 2 ligands (SSN, SO4), 6 pockets (best druggability 0.83). MolNFT v1 #111643 on GenesisL1: 3D structure…
- PDB
- 4YWU
- 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 · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Succinic semialdehyde dehydrogenase (EC 1.2.1.79) | protein | 455 | 44% helix, 21% strand | — |
Ligands and binding sites
- SSN · 4-oxobutanoic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.83 | 0.84 | 124 | empty |
| 2 | 400 | 0.63 | 0.77 | 42 | SO4 |
| 3 | 379 | 0.62 | 0.77 | 37 | SO4 |
| 4 | 204 | 0.56 | 0.79 | 25 | empty |
| 5 | 86 | 0.38 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2539 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 4YWU · 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 4YWU · PDBe 4YWU
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