MolNFT v1 · #16477 · protein
Human mitochondrial aldehyde dehydrogenase complexed with crotonaldehyde, NAD(H) and MG2+
1O01: “Human mitochondrial aldehyde dehydrogenase complexed with crotonaldehyde, NAD(H) and MG2+”. X-ray diffraction, 5 ligands (GAI, NAD, CRD), 20 pockets (best druggability 0.90). MolNFT v1 #16477 on GenesisL1: 3D structure, binding…
- PDB
- 1O01
- Type
- protein
- Length
- 3,953 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase
- EC
- 1.2.1.3
- UniProt
- P05091
- Ligands
- GAI, NAD, CRD, MG, NA
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, G, H | Aldehyde dehydrogenase (EC 1.2.1.3) | protein | 494 | 40% helix, 21% strand | P05091 |
| C | Aldehyde dehydrogenase (EC 1.2.1.3) | protein | 495 | 41% helix, 21% strand | P05091 |
Ligands and binding sites
- GAI · Guanidine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CRD · (2E)-but-2-enal · ligand · 6 copies · chains B, C, D, E, F, G
- MG · Magnesium ion · metal · 8 copies · chains C, D, E, F, G
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D, E, F, H, G
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 | 786 | 0.90 | 0.94 | 70 | empty |
| 2 | 817 | 0.90 | 0.93 | 72 | empty |
| 3 | 395 | 0.85 | 0.94 | 39 | empty |
| 4 | 359 | 0.85 | 0.94 | 38 | empty |
| 5 | 199 | 0.82 | 0.96 | 41 | EDO |
Interfaces
13 interfaces between chains.
- G–H · 2879 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 2878 Ų buried · 49 hydrogen bonds · protein-protein
- E–F · 2877 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 2861 Ų buried · 54 hydrogen bonds · protein-protein
- E–H · 1613 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 1O01 · Human mitochondrial aldehyde dehydrogenase complexed with crotonaldehyde, NAD(H) and Mg2+ · the same entry in another collection · chain H against H, TM-score 1.00
- P05091 · AlphaFold monomer V2.0 prediction for aldehyde dehydrogenase, mitochondrial (P05091) · a predicted model of the same protein · chain B 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 P05091
- Elsewhere: RCSB PDB 1O01 · PDBe 1O01 · UniProt P05091
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