Research workbench
The ternary structure of D-mandelate dehydrogenase with NADH and ANILINO(OXO)ACETATE
Analyse The ternary structure of D-mandelate dehydrogenase with NADH and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X20
- Type
- protein
- Length
- 1,671 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydropantoate 2-reductase
- EC
- 1.1.1.169
- UniProt
- Q3Y316
- Ligands
- NAD, AOT, SO4
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 2-dehydropantoate 2-reductase (EC 1.1.1.169) | protein | 312 | 49% helix, 17% strand | Q3Y316 |
| B | 2-dehydropantoate 2-reductase (EC 1.1.1.169) | protein | 309 | 52% helix, 17% strand | Q3Y316 |
| D | 2-dehydropantoate 2-reductase (EC 1.1.1.169) | protein | 244 | 54% helix, 9% strand | Q3Y316 |
| E | 2-dehydropantoate 2-reductase (EC 1.1.1.169) | protein | 310 | 49% helix, 17% strand | Q3Y316 |
| F | 2-dehydropantoate 2-reductase (EC 1.1.1.169) | protein | 184 | 58% helix, 6% strand | Q3Y316 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 5 copies · chains A, B, C, D, E
- AOT · 2-oxidanylidene-2-phenylazanyl-ethanoic acid · ligand · 5 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 18 copies · chains A, C, B, D, E
- GOL · Glycerol · additive · 18 copies · chains A, C, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.83 | 0.87 | 90 | GOL |
| 2 | 907 | 0.83 | 0.84 | 78 | NAD, AOT, GOL |
| 3 | 502 | 0.79 | 0.86 | 58 | NAD, AOT, GOL |
| 4 | 463 | 0.77 | 0.86 | 54 | NAD, AOT, GOL, SO4 |
| 5 | 609 | 0.77 | 0.83 | 55 | NAD, AOT, GOL |
Interfaces
8 interfaces between chains.
- A–B · 1064 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1059 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1058 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 859 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 569 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5X20 · The ternary structure of D-mandelate dehydrogenase with NADH and anilino(oxo)acetate · 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 Q3Y316
- Elsewhere: RCSB PDB 5X20 · PDBe 5X20 · UniProt Q3Y316
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