Research workbench
GAPN T244S mutant X-ray structure at 2.5 A
Analyse GAPN T244S mutant X-ray structure at 2.5 A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ID2
- Type
- protein
- Length
- 1,894 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Streptococcus mutans
- Molecule
- NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.9
- UniProt
- Q59931
- Ligands
- NAP, SO4
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.5 · 2 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.9) | protein | 473 | 43% helix, 23% strand | Q59931 |
| C, D | NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.9) | protein | 474 | 42% helix, 24% strand | Q59931 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.84 | 0.85 | 88 | empty |
| 2 | 720 | 0.83 | 0.87 | 75 | empty |
| 3 | 916 | 0.76 | 0.79 | 96 | SO4, NAP |
| 4 | 847 | 0.75 | 0.79 | 80 | SO4, NAP |
| 5 | 806 | 0.75 | 0.79 | 79 | SO4, NAP |
Interfaces
6 interfaces between chains.
- A–B · 2573 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2555 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 1170 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1159 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 816 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
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 2ID2 · PDBe 2ID2 · UniProt Q59931
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