MolNFT v1 · #114383 · protein
X-ray crystal structure of a aspartate-semialdehyde dehydrogenase bound to NADP from pseudomonas aeruginosa
5BNT: “X-ray crystal structure of a aspartate-semialdehyde dehydrogenase bound to NADP from pseudomonas aeruginosa”. X-ray diffraction, 1 ligand (NAP), 10 pockets (best druggability 0.75). MolNFT v1 #114383 on GenesisL1: 3D structure…
- PDB
- 5BNT
- Type
- protein
- Length
- 1,481 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
- Q51344
- Ligands
- NAP
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, B, D | Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 371 | 40% helix, 22% strand | Q51344 |
| A | Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 368 | 40% helix, 22% strand | Q51344 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains C, B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.75 | 0.78 | 110 | empty |
| 2 | 538 | 0.66 | 0.77 | 67 | NAP |
| 3 | 426 | 0.62 | 0.77 | 50 | NAP |
| 4 | 336 | 0.59 | 0.77 | 49 | NAP |
| 5 | 282 | 0.55 | 0.77 | 34 | empty |
Interfaces
5 interfaces between chains.
- A–D · 3642 Ų buried · 56 hydrogen bonds · protein-protein
- C–B · 3633 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 239 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 150 Ų buried · 1 hydrogen bond · protein-protein
- C–A · 141 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5BNT · X-ray Crystal Structure of a Aspartate-semialdehyde dehydrogenase bound to NADP from… · the same entry in another collection · chain D against D, TM-score 1.00
- Q51344 · AlphaFold monomer V2.0 prediction for aspartate-semialdehyde dehydrogenase (Q51344) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q51344
- Elsewhere: RCSB PDB 5BNT · PDBe 5BNT · UniProt Q51344
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