MolNFT v1 · #68886 · protein
Crystal structure of probable aldehyde dehydrogenase from listeria monocytogenes egd-E
3K9D: “Crystal structure of probable aldehyde dehydrogenase from listeria monocytogenes egd-E”. X-ray diffraction, 1 ligand (CL), 18 pockets (best druggability 0.75). MolNFT v1 #68886 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3K9D
- Type
- protein
- Length
- 1,815 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase
- UniProt
- Q8Y7U1
- Ligands
- CL
- Pockets
- 18 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aldehyde dehydrogenase | protein | 454 | 47% helix, 19% strand | Q8Y7U1 |
| C | Aldehyde dehydrogenase | protein | 454 | 46% helix, 18% strand | Q8Y7U1 |
| D | Aldehyde dehydrogenase | protein | 453 | 45% helix, 19% strand | Q8Y7U1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.75 | 0.79 | 100 | empty |
| 2 | 671 | 0.74 | 0.80 | 64 | empty |
| 3 | 600 | 0.73 | 0.81 | 60 | empty |
| 4 | 530 | 0.68 | 0.78 | 62 | empty |
| 5 | 547 | 0.67 | 0.78 | 62 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2815 Ų buried · 47 hydrogen bonds · protein-protein
- B–D · 2797 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 434 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 413 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 31 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3K9D · CRYSTAL STRUCTURE OF PROBABLE ALDEHYDE DEHYDROGENASE FROM Listeria monocytogenes EGD-e · 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 Q8Y7U1
- Elsewhere: RCSB PDB 3K9D · PDBe 3K9D · UniProt Q8Y7U1
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