MolNFT v1 · #26383 · protein
Escherichia COLI ydcw gene product is a medium-chain aldehyde dehydrogenase as determined by kinetics and crystal structure
1WND · Putative betaine aldehyde dehydrogenase: “Escherichia COLI ydcw gene product is a medium-chain aldehyde dehydrogenase as determined by kinetics and…”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 1WND
- 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
- CA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative betaine aldehyde dehydrogenase (EC 1.2.1.8) | protein | 474 | 41% helix, 24% strand | P77674 |
Ligands and binding sites
- CA · Calcium ion · metal · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.85 | 0.92 | 43 | empty |
| 2 | 375 | 0.85 | 0.94 | 33 | empty |
| 3 | 371 | 0.73 | 0.85 | 63 | empty |
| 4 | 309 | 0.72 | 0.85 | 47 | empty |
| 5 | 684 | 0.72 | 0.78 | 75 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2865 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 2849 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1128 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1073 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1014 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1WND · Escherichia coli YdcW gene product is a medium-chain aldehyde dehydrogenase as determined… · 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 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 P77674
- Elsewhere: RCSB PDB 1WND · PDBe 1WND · UniProt P77674
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