Research workbench
Crystal structure of aminoaldehyde dehydrogenase 1 from pisum sativum (PSAMADH1)
Analyse Crystal structure of aminoaldehyde dehydrogenase 1 from pisum sativum (PSAMADH1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IWK
- Type
- protein
- Length
- 5,952 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminoaldehyde dehydrogenase
- EC
- 1.2.1.19
- UniProt
- Q8VWZ1
- Ligands
- NAD, NA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, G, I, K | Aminoaldehyde dehydrogenase (EC 1.2.1.19) | protein | 496 | 40% helix, 20% strand | Q8VWZ1 |
| C, F | Aminoaldehyde dehydrogenase (EC 1.2.1.19) | protein | 495 | 40% helix, 20% strand | Q8VWZ1 |
| H, J | Aminoaldehyde dehydrogenase (EC 1.2.1.19) | protein | 497 | 41% helix, 20% strand | Q8VWZ1 |
| L | Aminoaldehyde dehydrogenase (EC 1.2.1.19) | protein | 496 | 40% helix, 20% strand | Q8VWZ1 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- NA · Sodium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- GOL · Glycerol · additive · 19 copies · chains A, B, C, F, G, H, I, J, K, L
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.87 | 0.88 | 108 | empty |
| 2 | 1175 | 0.86 | 0.87 | 111 | empty |
| 3 | 1180 | 0.86 | 0.87 | 113 | empty |
| 4 | 1193 | 0.85 | 0.87 | 122 | GOL |
| 5 | 1146 | 0.85 | 0.86 | 118 | GOL |
Interfaces
18 interfaces between chains.
- C–D · 4113 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 4108 Ų buried · 48 hydrogen bonds · protein-protein
- E–F · 4046 Ų buried · 52 hydrogen bonds · protein-protein
- I–J · 4040 Ų buried · 48 hydrogen bonds · protein-protein
- G–H · 4035 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 3IWK · Crystal structure of aminoaldehyde dehydrogenase 1 from Pisum sativum (PsAMADH1) · 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 Q8VWZ1
- Elsewhere: RCSB PDB 3IWK · PDBe 3IWK · UniProt Q8VWZ1
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