MolNFT v1 · #53163 · protein
Crystallographic structure of betaine aldehyde dehydrogenase from pseudomonas aeruginosa
2WME: “Crystallographic structure of betaine aldehyde dehydrogenase from pseudomonas aeruginosa”. X-ray diffraction, 2 ligands (NAP, K), 20 pockets (best druggability 0.85). MolNFT v1 #53163 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2WME
- Type
- protein
- Length
- 3,912 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Betaine aldehyde dehydrogenase
- EC
- 1.2.1.8
- UniProt
- Q9HTJ1
- Ligands
- NAP, K
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Betaine aldehyde dehydrogenase (EC 1.2.1.8) | protein | 489 | 43% helix, 22% strand | Q9HTJ1 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- K · Potassium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 21 copies · chains H, A, E, C, B, D, F, G
- BME · Beta-mercaptoethanol · additive · 5 copies · chains A, B, D, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.85 | 0.94 | 57 | K |
| 2 | 359 | 0.85 | 0.94 | 49 | K |
| 3 | 375 | 0.85 | 0.94 | 53 | K |
| 4 | 404 | 0.85 | 0.93 | 55 | K |
| 5 | 1019 | 0.82 | 0.83 | 107 | GOL |
Interfaces
14 interfaces between chains.
- A–B · 3572 Ų buried · 58 hydrogen bonds · protein-protein
- G–H · 3562 Ų buried · 52 hydrogen bonds · protein-protein
- E–F · 3561 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 3557 Ų buried · 55 hydrogen bonds · protein-protein
- B–C · 1219 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (additive adduct, oxidation).
Compared structures
- 2WME · Crystallographic structure of betaine aldehyde dehydrogenase from Pseudomonas aeruginosa · the same entry in another collection · chain H against H, 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 G 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 2WME · PDBe 2WME · UniProt Q9HTJ1
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