Research workbench
Crystal structure of canton G6PD in complex with structural NADP
Analyse Crystal structure of canton G6PD in complex with structural NADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E07
- Type
- protein
- Length
- 3,889 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-6-phosphate 1-dehydrogenase
- EC
- 1.1.1.49
- UniProt
- P11413
- Ligands
- NAP, PO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, F, N, T, W | Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) | protein | 486 | 39% helix, 22% strand | P11413 |
| C | Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) | protein | 487 | 40% helix, 22% strand | P11413 |
| Q | Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) | protein | 487 | 39% helix, 21% strand | P11413 |
| B | Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) | protein | 485 | 40% helix, 22% strand | P11413 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains L, C, F, N, Q, T, W, B
- PO4 · Phosphate ion · ion · 8 copies · chains L, C, F, N, Q, T, W, B
- GOL · Glycerol · additive · 29 copies · chains L, N, B, C, F, Q, T, W
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.87 | 0.88 | 124 | GOL |
| 2 | 1093 | 0.87 | 0.88 | 124 | empty |
| 3 | 646 | 0.76 | 0.81 | 72 | empty |
| 4 | 678 | 0.74 | 0.80 | 78 | NAP |
| 5 | 463 | 0.70 | 0.80 | 46 | empty |
Interfaces
16 interfaces between chains.
- L–C · 2916 Ų buried · 56 hydrogen bonds · protein-protein
- F–W · 2890 Ų buried · 50 hydrogen bonds · protein-protein
- N–B · 2889 Ų buried · 52 hydrogen bonds · protein-protein
- Q–T · 2858 Ų buried · 51 hydrogen bonds · protein-protein
- L–Q · 901 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6E07 · Crystal structure of Canton G6PD in complex with structural NADP · the same entry in another collection · chain B against B, TM-score 1.00
- P11413 · AlphaFold monomer V2.0 prediction for glucose-6-phosphate 1-dehydrogenase (P11413) · a predicted model of the same protein · chain L 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 P11413
- Elsewhere: RCSB PDB 6E07 · PDBe 6E07 · UniProt P11413
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