Research workbench
Crystal structure of the NADP+ dependent aldehyde dehydrogenase from vibrio harveyi.
Analyse Crystal structure of the NADP+ dependent aldehyde dehydrogenase from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EZ0
- Type
- protein
- Length
- 2,010 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase
- EC
- 1.2.1.5
- UniProt
- Q56694
- Ligands
- NAP
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldehyde dehydrogenase (EC 1.2.1.5) | protein | 504 | 44% helix, 19% strand | Q56694 |
| B, C, D | Aldehyde dehydrogenase (EC 1.2.1.5) | protein | 502 | 44% helix, 20% strand | Q56694 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 715 | 0.84 | 0.88 | 66 | empty |
| 2 | 765 | 0.84 | 0.87 | 63 | empty |
| 3 | 603 | 0.77 | 0.83 | 84 | empty |
| 4 | 580 | 0.76 | 0.82 | 85 | empty |
| 5 | 911 | 0.74 | 0.77 | 103 | NAP |
Interfaces
4 interfaces between chains.
- A–D · 3071 Ų buried · 58 hydrogen bonds · protein-protein
- B–C · 3067 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 76 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1EZ0 · Crystal structure of the NADP+ dependent aldehyde dehydrogenase from vibrio harveyi. · the same entry in another collection · chain D against D, TM-score 1.00
- Q56694 · AlphaFold monomer V2.0 prediction for NADP-dependent fatty aldehyde dehydrogenase (Q56694) · a predicted model of the same protein · chain B 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 Q56694
- Elsewhere: RCSB PDB 1EZ0 · PDBe 1EZ0 · UniProt Q56694
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