Research workbench
Crystal structure of aar with NADPH and stearyl in complex with ado binding a long chain carbohydrate
Analyse Crystal structure of aar with NADPH and stearyl in complex with ado binding a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JZY
- Type
- protein
- Length
- 560 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Long-chain acyl-[acyl-carrier-protein] reductase; Aldehyde decarbonylase
- EC
- 1.2.1.80, 4.1.99.5
- UniProt
- Q54765, Q8KPT4
- Ligands
- NDP, OCD, PL3, FE2
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Long-chain acyl-[acyl-carrier-protein] reductase (EC 1.2.1.80) | protein | 342 | 40% helix, 21% strand | Q54765 |
| B | Aldehyde decarbonylase (EC 4.1.99.5) | protein | 218 | 86% helix, 0% strand | Q8KPT4 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- OCD · octadecanal · ligand · chains A, B
- PL3 · Hexadecan-1-ol · ligand · chains B
- FE2 · Fe (II) ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.83 | 0.98 | 35 | PL3 |
| 2 | 434 | 0.82 | 0.89 | 74 | NDP, OCD |
| 3 | 258 | 0.52 | 0.75 | 26 | empty |
| 4 | 121 | 0.41 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 962 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6JZY · Crystal structure of AAR with NADPH and stearyl in complex with ADO binding a long chain… · the same entry in another collection · chain A against A, TM-score 1.00
- Q54765 · AlphaFold monomer V2.0 prediction for long-chain acyl-[acyl-carrier- protein] reductase… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q54765
- Every structure of UniProt Q8KPT4
- Elsewhere: RCSB PDB 6JZY · PDBe 6JZY · UniProt Q54765 · UniProt Q8KPT4
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