MolNFT v1 · #177094 · protein
The structure of cytosolic tapgi with substrate
7E78 · Glucose-6-phosphate isomerase: “The structure of cytosolic tapgi with substrate”. X-ray diffraction, 1 ligand (G6P), 20 pockets (best druggability 0.82). MolNFT v1 #177094 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7E78
- Type
- protein
- Length
- 2,247 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-6-phosphate isomerase
- EC
- 5.3.1.9
- UniProt
- Q1PBI3
- Ligands
- G6P
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glucose-6-phosphate isomerase (EC 5.3.1.9) | protein | 562 | 52% helix, 12% strand | Q1PBI3 |
| C | Glucose-6-phosphate isomerase (EC 5.3.1.9) | protein | 562 | 52% helix, 12% strand | Q1PBI3 |
| D | Glucose-6-phosphate isomerase (EC 5.3.1.9) | protein | 561 | 54% helix, 11% strand | Q1PBI3 |
Ligands and binding sites
- G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.82 | 0.83 | 90 | empty |
| 2 | 698 | 0.81 | 0.85 | 57 | empty |
| 3 | 433 | 0.72 | 0.82 | 50 | empty |
| 4 | 214 | 0.71 | 0.88 | 35 | empty |
| 5 | 456 | 0.71 | 0.82 | 45 | empty |
Interfaces
4 interfaces between chains.
- B–D · 6982 Ų buried · 102 hydrogen bonds · protein-protein
- A–C · 6909 Ų buried · 106 hydrogen bonds · protein-protein
- A–D · 416 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 31 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7E78 · the structure of cytosolic TaPGI with substrate · the same entry in another collection · 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 Q1PBI3
- Elsewhere: RCSB PDB 7E78 · PDBe 7E78 · UniProt Q1PBI3
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