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The crystal structure of the aldehyde dehydrogenase kaub from pseudomonas aeruginosa
Analyse The crystal structure of the aldehyde dehydrogenase kaub from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B4R
- Type
- protein
- Length
- 1,982 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kaub
- EC
- 1.2.1.54
- UniProt
- Q9HTP2
- Ligands
- TOE, K
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kaub (EC 1.2.1.54) | protein | 497 | 43% helix, 21% strand | Q9HTP2 |
| B, C, D | Kaub (EC 1.2.1.54) | protein | 495 | 43% helix, 21% strand | Q9HTP2 |
Ligands and binding sites
- TOE · 2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxyl · ligand · 3 copies · chains A, B, C
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, D, C
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.84 | 0.92 | 41 | empty |
| 2 | 257 | 0.83 | 0.95 | 36 | empty |
| 3 | 269 | 0.82 | 0.94 | 34 | empty |
| 4 | 276 | 0.82 | 0.93 | 36 | empty |
| 5 | 264 | 0.81 | 0.93 | 36 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2600 Ų buried · 52 hydrogen bonds · protein-protein
- C–D · 2560 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 1084 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1062 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1003 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 6B4R · The crystal structure of the aldehyde dehydrogenase KauB from Pseudomonas aeruginosa · the same entry in another collection · chain A 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 Q9HTP2
- Elsewhere: RCSB PDB 6B4R · PDBe 6B4R · UniProt Q9HTP2
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