MolNFT v1 · #14496 · protein
Crystal structure of aspartate semialdehyde dehydrogenase from vibrio cholerae with NADP and S-methyl-L-cysteine sulfoxide
1MB4 · Aspartate-semialdehyde dehydrogenase: “Crystal structure of aspartate semialdehyde dehydrogenase from vibrio cholerae with NADP and…”. X-ray diffraction, 2 ligands (CYS, NDP), 5 pockets (best druggability 0.63). MolNFT v1 #14496 on…
- PDB
- 1MB4
- Type
- protein
- Length
- 738 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate-semialdehyde dehydrogenase
- EC
- 1.2.1.11
- UniProt
- Q9KQG2
- Ligands
- CYS, NDP
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 369 | 41% helix, 23% strand | Q9KQG2 |
Ligands and binding sites
- CYS · Cysteine · ligand · 2 copies · chains A, B
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.63 | 0.77 | 50 | CYS, NDP |
| 2 | 339 | 0.60 | 0.78 | 45 | CYS, NDP |
| 3 | 84 | 0.38 | 0.76 | 14 | empty |
| 4 | 75 | 0.34 | 0.75 | 15 | empty |
| 5 | 56 | 0.29 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3492 Ų buried · 62 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1MB4 · Crystal structure of aspartate semialdehyde dehydrogenase from vibrio cholerae with NADP… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KQG2 · AlphaFold monomer V2.0 prediction for aspartate-semialdehyde dehydrogenase 1 (Q9KQG2) · a predicted model of the same protein · chain B 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 Q9KQG2
- Elsewhere: RCSB PDB 1MB4 · PDBe 1MB4 · UniProt Q9KQG2
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