Research workbench
Glucose-6-phosphate isomerase from francisella tularensis complexed with ribose 1,5-bisphosphate.
Analyse Glucose-6-phosphate isomerase from francisella tularensis complexed with ribose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q88
- Type
- protein
- Length
- 541 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-6-phosphate isomerase
- EC
- 5.3.1.9
- UniProt
- Q5NFC4
- Ligands
- RI2, CA, PO4
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-6-phosphate isomerase (EC 5.3.1.9) | protein | 541 | 55% helix, 13% strand | Q5NFC4 |
Ligands and binding sites
- RI2 · 1,5-di-O-phosphono-alpha-D-ribofuranose · ligand · chains A
- CA · Calcium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A
- IPA · Isopropyl alcohol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.63 | 0.79 | 41 | RI2 |
| 2 | 62 | 0.51 | 0.86 | 16 | empty |
| 3 | 64 | 0.45 | 0.83 | 16 | empty |
| 4 | 69 | 0.29 | 0.73 | 17 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3Q88 · Glucose-6-phosphate isomerase from Francisella tularensis complexed with ribose… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5NFC4 · AlphaFold monomer V2.0 prediction for glucose-6-phosphate isomerase (Q5NFC4) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q5NFC4
- Elsewhere: RCSB PDB 3Q88 · PDBe 3Q88 · UniProt Q5NFC4
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