MolNFT v1 · #18496 · protein
Crystal structure of the H277N mutant of aspartate semialdehyde dehydrogenase from haemophilus influenzae bound with NADP, S-methyl cysteine sulfoxide and cacodylate
1PQU · Aspartate-semialdehyde dehydrogenase: “Crystal structure of the H277N mutant of aspartate semialdehyde dehydrogenase from haemophilus influenzae…”. X-ray diffraction, 2 ligands (CYS, NAP), 16 pockets (best druggability 0.70). MolNFT…
- PDB
- 1PQU
- Type
- protein
- Length
- 1,469 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate-semialdehyde dehydrogenase
- EC
- 1.2.1.11
- UniProt
- P44801
- Ligands
- CYS, NAP
- Pockets
- 16 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 371 | 40% helix, 24% strand | P44801 |
| C | Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 356 | 43% helix, 25% strand | P44801 |
Ligands and binding sites
- CYS · Cysteine · ligand · 4 copies · chains A, B, C, D
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B, D
- CAC · Cacodylate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.70 | 0.77 | 89 | empty |
| 2 | 487 | 0.66 | 0.78 | 59 | CAC, NAP, CYS |
| 3 | 456 | 0.64 | 0.78 | 56 | CAC, NAP, CYS |
| 4 | 414 | 0.64 | 0.78 | 47 | CAC, CYS |
| 5 | 292 | 0.61 | 0.79 | 31 | CAC, NAP, CYS |
Interfaces
5 interfaces between chains.
- B–C · 3478 Ų buried · 43 hydrogen bonds · protein-protein
- A–D · 3477 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 241 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 204 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 80 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1PQU · Crystal Structure of the H277N Mutant of Aspartate Semialdehyde Dehydrogenase from… · the same entry in another collection · chain D against D, TM-score 1.00
- P44801 · AlphaFold monomer V2.0 prediction for aspartate-semialdehyde dehydrogenase (P44801) · 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 P44801
- Elsewhere: RCSB PDB 1PQU · PDBe 1PQU · UniProt P44801
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