Research workbench
Ternary complex of an NADP dependent aldehyde dehydrogenase
Analyse Ternary complex of an NADP dependent aldehyde dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QI1
- Type
- protein
- Length
- 1,896 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (NADP-dependent nonphosphorylating glyceraldehyde- 3-phosphate dehydrogenase)
- EC
- 1.2.1.9
- UniProt
- Q59931
- Ligands
- NAP, G3H, G3P
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protein (NADP-dependent nonphosphorylating glyceraldehyde- 3-phosphate dehydrogenase) (EC 1.2.1.9) | protein | 474 | 42% helix, 23% strand | Q59931 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- G3H · Glyceraldehyde-3-phosphate · ligand · 3 copies · chains A, C, D
- G3P · Sn-glycerol-3-phosphate · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 753 | 0.83 | 0.86 | 75 | empty |
| 2 | 739 | 0.83 | 0.86 | 77 | empty |
| 3 | 815 | 0.72 | 0.77 | 76 | NAP, G3P |
| 4 | 820 | 0.72 | 0.77 | 79 | NAP, G3H |
| 5 | 813 | 0.71 | 0.77 | 75 | NAP, G3H |
Interfaces
6 interfaces between chains.
- A–B · 2427 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2411 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1142 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1136 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 841 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1QI1 · Ternary Complex of an NADP Dependent Aldehyde Dehydrogenase · the same entry in another collection · chain D against D, TM-score 1.00
- Q59931 · AlphaFold monomer V2.0 prediction for NADP-dependent glyceraldehyde-3-phosphate… · a predicted model of the same protein · chain D 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 Q59931
- Elsewhere: RCSB PDB 1QI1 · PDBe 1QI1 · UniProt Q59931
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