MolNFT v1 · #62450 · protein
Crystal structure of a putative succinate-semialdehyde dehydrogenase from salmonella typhimurium LT2 with bound NAD
3EFV: “Crystal structure of a putative succinate-semialdehyde dehydrogenase from salmonella typhimurium LT2 with…”. X-ray diffraction, 1 ligand (NAD), 17 pockets (best druggability 0.84). MolNFT v1 #62450 on GenesisL1: 3D structure…
- PDB
- 3EFV
- Type
- protein
- Length
- 1,831 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative succinate-semialdehyde dehydrogenase
- EC
- 1.2.1.-
- UniProt
- Q8ZPI3
- Ligands
- NAD
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative succinate-semialdehyde dehydrogenase (EC 1.2.1.-) | protein | 459 | 44% helix, 22% strand | Q8ZPI3 |
| B | Putative succinate-semialdehyde dehydrogenase (EC 1.2.1.-) | protein | 458 | 44% helix, 21% strand | Q8ZPI3 |
| C, D | Putative succinate-semialdehyde dehydrogenase (EC 1.2.1.-) | protein | 457 | 45% helix, 21% strand | Q8ZPI3 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1189 | 0.84 | 0.85 | 148 | NAD |
| 2 | 702 | 0.84 | 0.87 | 102 | empty |
| 3 | 1109 | 0.83 | 0.83 | 128 | empty |
| 4 | 456 | 0.76 | 0.85 | 60 | NAD |
| 5 | 426 | 0.76 | 0.85 | 64 | NAD |
Interfaces
4 interfaces between chains.
- A–B · 2524 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2506 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 1133 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1100 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 49 modified (engineered).
Compared structures
- 3EFV · Crystal Structure of a Putative Succinate-Semialdehyde Dehydrogenase from Salmonella… · 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 Q8ZPI3
- Elsewhere: RCSB PDB 3EFV · PDBe 3EFV · UniProt Q8ZPI3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.