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2.0 ångström resolution crystal structure of glucose-6-phosphate isomerase (pgi) from bacillus anthracis.
Analyse 2.0 ångström resolution crystal structure of glucose-6-phosphate isomerase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IFS
- Type
- protein
- Length
- 2,692 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-6-phosphate isomerase
- EC
- 5.3.1.9
- UniProt
- Q81K75
- Ligands
- LI, SO4, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Glucose-6-phosphate isomerase (EC 5.3.1.9) | protein | 449 | 55% helix, 12% strand | Q81K75 |
| B, C, F | Glucose-6-phosphate isomerase (EC 5.3.1.9) | protein | 448 | 55% helix, 13% strand | Q81K75 |
| E | Glucose-6-phosphate isomerase (EC 5.3.1.9) | protein | 450 | 55% helix, 12% strand | Q81K75 |
Ligands and binding sites
- LI · Lithium ion · metal · chains C, F
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, F
- CL · Chloride ion · ion · chains B
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.87 | 0.88 | 104 | empty |
| 2 | 881 | 0.86 | 0.88 | 80 | empty |
| 3 | 1028 | 0.86 | 0.87 | 107 | empty |
| 4 | 305 | 0.77 | 0.89 | 50 | empty |
| 5 | 312 | 0.75 | 0.87 | 47 | empty |
Interfaces
9 interfaces between chains.
- C–D · 5903 Ų buried · 85 hydrogen bonds · protein-protein
- A–B · 5871 Ų buried · 87 hydrogen bonds · protein-protein
- E–F · 5795 Ų buried · 84 hydrogen bonds · protein-protein
- B–C · 881 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 879 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 49 modified (engineered).
Compared structures
- 3IFS · 2.0 Angstrom Resolution Crystal Structure of Glucose-6-phosphate Isomerase (pgi) from… · the same entry in another collection · chain F against F, TM-score 1.00
- Q81K75 · AlphaFold monomer V2.0 prediction for glucose-6-phosphate isomerase (Q81K75) · a predicted model of the same protein · chain D 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 Q81K75
- Elsewhere: RCSB PDB 3IFS · PDBe 3IFS · UniProt Q81K75
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