Research workbench
Ovis aries aldehyde dehydrogenase 1A1 in complex with a duocarmycin analog
Analyse Ovis aries aldehyde dehydrogenase 1A1 in complex with a duocarmycin analog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AC0
- Type
- protein
- Length
- 988 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinal dehydrogenase 1
- EC
- 1.2.1.36
- UniProt
- P51977
- Ligands
- NAD, K9P, MG
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Retinal dehydrogenase 1 (EC 1.2.1.36) | protein | 494 | 41% helix, 21% strand | P51977 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- K9P · 1-[(1S)-1-methyl-5-oxidanyl-1,2-dihydrobenzo[e]indol-3-yl]hexan-1-one · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.84 | 0.90 | 40 | empty |
| 2 | 692 | 0.74 | 0.80 | 79 | NAD, K9P, MG |
| 3 | 630 | 0.74 | 0.80 | 65 | NAD, K9P, MG |
| 4 | 197 | 0.62 | 0.83 | 34 | empty |
| 5 | 176 | 0.60 | 0.83 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 2957 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5AC0 · ovis aries Aldehyde Dehydrogenase 1A1 in complex with a duocarmycin analog · the same entry in another collection · chain A against A, TM-score 1.00
- P51977 · AlphaFold monomer V2.0 prediction for retinal dehydrogenase 1 (P51977) · 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 P51977
- Elsewhere: RCSB PDB 5AC0 · PDBe 5AC0 · UniProt P51977
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