MolNFT v1 · #127523 · protein
Crystal structure of aldehyde dehydrogenase 21 (ALDH21) from physcomitrella patens in its apoform
5MZ5: “Crystal structure of aldehyde dehydrogenase 21 (ALDH21) from physcomitrella patens in its apoform”. X-ray diffraction, 17 pockets (best druggability 0.81). MolNFT v1 #127523 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5MZ5
- Type
- protein
- Length
- 1,922 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ALDH21)
- UniProt
- A9SS48
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | ALDH21) | protein | 481 | 40% helix, 23% strand | A9SS48 |
| B, D | ALDH21) | protein | 480 | 40% helix, 23% strand | A9SS48 |
Ligands and binding sites
- GOL · Glycerol · additive · 12 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.81 | 0.88 | 48 | GOL, EDO |
| 2 | 431 | 0.81 | 0.89 | 42 | GOL |
| 3 | 764 | 0.77 | 0.81 | 80 | empty |
| 4 | 730 | 0.77 | 0.82 | 71 | empty |
| 5 | 766 | 0.77 | 0.81 | 78 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2837 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 2833 Ų buried · 46 hydrogen bonds · protein-protein
- A–D · 1193 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1184 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 965 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5MZ5 · Crystal structure of aldehyde dehydrogenase 21 (ALDH21) from Physcomitrella patens in its… · 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 A9SS48
- Elsewhere: RCSB PDB 5MZ5 · PDBe 5MZ5 · UniProt A9SS48
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