Research workbench
Crystal structure of aldehyde dehydrogenase 21 (ALDH21) from physcomitrella patens in complex with NADP+
Analyse Crystal structure of aldehyde dehydrogenase 21 (ALDH21) from physcomitrella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N5S
- Type
- protein
- Length
- 1,922 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase 21 (ALDH21)
- UniProt
- A9SS48
- Ligands
- NAP
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Aldehyde dehydrogenase 21 (ALDH21) | protein | 480 | 40% helix, 23% strand | A9SS48 |
| B, C | Aldehyde dehydrogenase 21 (ALDH21) | protein | 481 | 40% helix, 22% strand | A9SS48 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, D, C
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 | 762 | 0.79 | 0.83 | 55 | EDO |
| 2 | 762 | 0.77 | 0.82 | 54 | empty |
| 3 | 835 | 0.71 | 0.76 | 68 | empty |
| 4 | 409 | 0.67 | 0.80 | 50 | NAP |
| 5 | 462 | 0.67 | 0.79 | 56 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2870 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2859 Ų buried · 47 hydrogen bonds · protein-protein
- B–D · 249 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5N5S · Crystal structure of aldehyde dehydrogenase 21 (ALDH21) from Physcomitrella patens in… · the same entry in another collection · chain B against B, 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 A9SS48
- Elsewhere: RCSB PDB 5N5S · PDBe 5N5S · UniProt A9SS48
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