Research workbench
Thioacylenzyme intermediate of gapn from S. mutans, new data integration and refinement.
Analyse Thioacylenzyme intermediate of gapn from S. mutans, new data integration and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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