Research workbench
Crystal structure of (S)-3-hydroxybutyryl-CoA dehydrogenase PAAH1 in complex with NAD+
Analyse Crystal structure of (S)-3-hydroxybutyryl-CoA dehydrogenase PAAH1 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PZD
- Type
- protein
- Length
- 2,547 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxyacyl-CoA dehydrogenase
- EC
- 1.1.1.35
- UniProt
- Q0KEY8
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I | 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) | protein | 283 | 50% helix, 16% strand | Q0KEY8 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 9 copies · chains A, C, B, D, F, E, G, I, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.81 | 0.82 | 106 | empty |
| 2 | 56 | 0.72 | 0.99 | 20 | empty |
| 3 | 60 | 0.70 | 0.97 | 19 | empty |
| 4 | 366 | 0.65 | 0.80 | 54 | NAD |
| 5 | 363 | 0.63 | 0.79 | 52 | NAD |
Interfaces
13 interfaces between chains.
- D–G · 1963 Ų buried · 26 hydrogen bonds · protein-protein
- H–I · 1962 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1959 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1945 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 516 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4PZD · Crystal structure of (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1 in complex with NAD+ · 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 Q0KEY8
- Elsewhere: RCSB PDB 4PZD · PDBe 4PZD · UniProt Q0KEY8
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