Research workbench
Structure of aldehyde dehydrogenase 12 (ALDH12) from zea mays
Analyse Structure of aldehyde dehydrogenase 12 (ALDH12) from zea mays in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D97
- Type
- protein
- Length
- 2,087 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase 12
- EC
- 1.2.1.88
- UniProt
- A0A2H4PMI3
- Ligands
- NAD
- Pockets
- 19 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Aldehyde dehydrogenase 12 (EC 1.2.1.88) | protein | 522 | 37% helix, 20% strand | A0A2H4PMI3 |
| C | Aldehyde dehydrogenase 12 (EC 1.2.1.88) | protein | 521 | 36% helix, 21% strand | A0A2H4PMI3 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 891 | 0.74 | 0.78 | 90 | NAD |
| 2 | 472 | 0.73 | 0.82 | 44 | empty |
| 3 | 538 | 0.73 | 0.81 | 63 | NAD |
| 4 | 462 | 0.72 | 0.82 | 51 | empty |
| 5 | 495 | 0.72 | 0.81 | 51 | empty |
Interfaces
5 interfaces between chains.
- C–D · 3874 Ų buried · 75 hydrogen bonds · protein-protein
- A–B · 3867 Ų buried · 75 hydrogen bonds · protein-protein
- B–D · 440 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 435 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 297 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6D97 · Structure of aldehyde dehydrogenase 12 (ALDH12) from Zea mays · 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 A0A2H4PMI3
- Elsewhere: RCSB PDB 6D97 · PDBe 6D97 · UniProt A0A2H4PMI3
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