MolNFT v1 · #54074 · protein
Crystallographic structure of betaine aldehyde dehydrogenase mutant E252A from pseudomonas aeruginosa
2XDR: “Crystallographic structure of betaine aldehyde dehydrogenase mutant E252A from pseudomonas aeruginosa”. X-ray diffraction, 3 ligands (NDP, TOE, K), 13 pockets (best druggability 0.85). MolNFT v1 #54074 on GenesisL1: 3D structure…
- PDB
- 2XDR
- Type
- protein
- Length
- 1,956 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Betaine aldehyde dehydrogenase
- EC
- 1.2.1.8
- UniProt
- Q9HTJ1
- Ligands
- NDP, TOE, K
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Betaine aldehyde dehydrogenase (EC 1.2.1.8) | protein | 489 | 44% helix, 22% strand | Q9HTJ1 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- TOE · 2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxyl · ligand · chains A
- K · Potassium ion · metal · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 14 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.85 | 0.94 | 55 | K |
| 2 | 329 | 0.84 | 0.94 | 52 | K |
| 3 | 1057 | 0.82 | 0.83 | 101 | GOL |
| 4 | 1163 | 0.80 | 0.81 | 104 | GOL |
| 5 | 1153 | 0.80 | 0.81 | 103 | GOL |
Interfaces
6 interfaces between chains.
- A–B · 3535 Ų buried · 56 hydrogen bonds · protein-protein
- C–D · 3471 Ų buried · 57 hydrogen bonds · protein-protein
- B–C · 1143 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1134 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 811 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2XDR · Crystallographic structure of betaine aldehyde dehydrogenase mutant E252A from… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9HTJ1 · AlphaFold monomer V2.0 prediction for NAD/NADP-dependent betaine aldehyde dehydrogenase… · a predicted model of the same protein · chain C 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 Q9HTJ1
- Elsewhere: RCSB PDB 2XDR · PDBe 2XDR · UniProt Q9HTJ1
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