Research workbench
X-ray crystal structure of a putative phenylacetaldehyde dehydrogenase from burkholderia cenocepacia
Analyse X-ray crystal structure of a putative phenylacetaldehyde dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O5H
- Type
- protein
- Length
- 2,014 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylacetaldehyde dehydrogenase
- EC
- 1.2.1.39
- UniProt
- B4EH14
- Ligands
- NA
- Pockets
- 18 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phenylacetaldehyde dehydrogenase (EC 1.2.1.39) | protein | 511 | 41% helix, 22% strand | B4EH14 |
| C, D | Phenylacetaldehyde dehydrogenase (EC 1.2.1.39) | protein | 496 | 42% helix, 22% strand | B4EH14 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.88 | 0.90 | 76 | empty |
| 2 | 553 | 0.85 | 0.90 | 49 | empty |
| 3 | 757 | 0.78 | 0.82 | 64 | empty |
| 4 | 788 | 0.78 | 0.82 | 59 | empty |
| 5 | 798 | 0.77 | 0.81 | 61 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2801 Ų buried · 51 hydrogen bonds · protein-protein
- B–C · 2774 Ų buried · 52 hydrogen bonds · protein-protein
- B–D · 1250 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1237 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1074 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 4O5H · X-ray crystal structure of a putative phenylacetaldehyde dehydrogenase from Burkholderia… · 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 B4EH14
- Elsewhere: RCSB PDB 4O5H · PDBe 4O5H · UniProt B4EH14
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