MolNFT v1 · #49106 · protein
Thioacylenzyme intermediate of gapn from S. mutans, new data integration and refinement.
2QE0 · NADP-dependent glyceraldehyde-3-phosphate dehydrogenase: “Thioacylenzyme intermediate of gapn from S. mutans, new data integration and refinement.”. X-ray diffraction, 2 ligands (G3H, NAP), 14 pockets (best druggability 0.84).…
- PDB
- 2QE0
- Type
- protein
- Length
- 1,896 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.9
- UniProt
- Q59931
- Ligands
- G3H, NAP
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.9) | protein | 474 | 43% helix, 24% strand | Q59931 |
Ligands and binding sites
- G3H · Glyceraldehyde-3-phosphate · ligand · 4 copies · chains A, B, C, D
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.84 | 0.87 | 79 | empty |
| 2 | 790 | 0.84 | 0.87 | 75 | empty |
| 3 | 437 | 0.76 | 0.85 | 44 | empty |
| 4 | 856 | 0.74 | 0.78 | 91 | G3H, NAP |
| 5 | 814 | 0.72 | 0.77 | 85 | G3H, NAP |
Interfaces
6 interfaces between chains.
- C–D · 2628 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2609 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1159 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1159 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 830 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 2QE0 · Thioacylenzyme Intermediate of GAPN from S. Mutans, New Data Integration and Refinement. · 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 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 Q59931
- Elsewhere: RCSB PDB 2QE0 · PDBe 2QE0 · UniProt Q59931
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.