Research workbench
Crystal structure of aldehyde dehydrogenase 21 (ALDH21) from physcomitrella patens in complex with the reaction product succinate
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
- 5MZ8
- Type
- protein
- Length
- 1,923 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase 21
- UniProt
- A9SS48
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Aldehyde dehydrogenase 21 | protein | 481 | 39% helix, 23% strand | A9SS48 |
| B | Aldehyde dehydrogenase 21 | protein | 480 | 39% helix, 23% strand | A9SS48 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 41 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, D, B, C
- SIN · Succinic acid · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.81 | 0.88 | 47 | EDO, GOL |
| 2 | 429 | 0.81 | 0.89 | 42 | EDO |
| 3 | 780 | 0.77 | 0.81 | 81 | EDO |
| 4 | 764 | 0.77 | 0.82 | 76 | EDO, PEG |
| 5 | 756 | 0.77 | 0.82 | 72 | EDO |
Interfaces
6 interfaces between chains.
- C–D · 2844 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2839 Ų buried · 47 hydrogen bonds · protein-protein
- A–D · 1184 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1178 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 955 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5MZ8 · 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 5MZ8 · PDBe 5MZ8 · UniProt A9SS48
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