MolNFT v1 · #144112 · protein
Apo form of the E124S mutant of betaine aldehyde dehydrogenase from pseudomonas aeruginosa
6BJP · NAD/NADP-dependent betaine aldehyde dehydrogenase: “Apo form of the E124S mutant of betaine aldehyde dehydrogenase from pseudomonas aeruginosa”. X-ray diffraction, 1 ligand (K), 16 pockets (best druggability 0.77). MolNFT v1 #144112…
- PDB
- 6BJP
- Type
- protein
- Length
- 1,850 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD/NADP-dependent betaine aldehyde dehydrogenase
- EC
- 1.2.1.8
- UniProt
- Q9HTJ1
- Ligands
- K
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD/NADP-dependent betaine aldehyde dehydrogenase (EC 1.2.1.8) | protein | 460 | 42% helix, 20% strand | Q9HTJ1 |
| B | NAD/NADP-dependent betaine aldehyde dehydrogenase (EC 1.2.1.8) | protein | 466 | 42% helix, 21% strand | Q9HTJ1 |
| C | NAD/NADP-dependent betaine aldehyde dehydrogenase (EC 1.2.1.8) | protein | 463 | 42% helix, 21% strand | Q9HTJ1 |
| D | NAD/NADP-dependent betaine aldehyde dehydrogenase (EC 1.2.1.8) | protein | 461 | 42% helix, 20% strand | Q9HTJ1 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, D, B
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.77 | 0.79 | 128 | EDO |
| 2 | 730 | 0.70 | 0.77 | 81 | empty |
| 3 | 329 | 0.55 | 0.75 | 43 | empty |
| 4 | 136 | 0.45 | 0.76 | 28 | empty |
| 5 | 175 | 0.42 | 0.74 | 26 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2658 Ų buried · 45 hydrogen bonds · protein-protein
- A–D · 2617 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 275 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 231 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 169 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 6BJP · Apo form of the E124S mutant of betaine aldehyde dehydrogenase from Pseudomonas aeruginosa · the same entry in another collection · chain A against A, 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 D against A, TM-score 0.96
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 6BJP · PDBe 6BJP · UniProt Q9HTJ1
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