Research workbench
Escherichia COLI ydcw gene product is a medium-chain aldehyde dehydrogenase (complexed with NADH and betaine aldehyde)
Analyse Escherichia COLI ydcw gene product is a medium-chain aldehyde dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WNB
- Type
- protein
- Length
- 1,896 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative betaine aldehyde dehydrogenase
- EC
- 1.2.1.8
- UniProt
- P77674
- Ligands
- NAI, BTL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative betaine aldehyde dehydrogenase (EC 1.2.1.8) | protein | 474 | 40% helix, 23% strand | P77674 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- BTL · Betaine aldehyde · ligand · 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.86 | 0.94 | 33 | empty |
| 2 | 379 | 0.86 | 0.94 | 32 | empty |
| 3 | 734 | 0.74 | 0.79 | 89 | BTL, NAI |
| 4 | 708 | 0.74 | 0.79 | 80 | NAI |
| 5 | 658 | 0.73 | 0.80 | 79 | NAI |
Interfaces
6 interfaces between chains.
- A–C · 2866 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 2866 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1105 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1104 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1063 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1WNB · Escherichia coli YdcW gene product is a medium-chain aldehyde dehydrogenase (complexed… · the same entry in another collection · chain D against D, TM-score 1.00
- P77674 · AlphaFold monomer V2.0 prediction for gamma-aminobutyraldehyde dehydrogenase (P77674) · a predicted model of the same protein · 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 P77674
- Elsewhere: RCSB PDB 1WNB · PDBe 1WNB · UniProt P77674
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