Research workbench
Crystal structure of the exocytosis-sensitive phosphoprotein, PP63/PARAFUSIN (phosphoglucomutase) from paramecium
Analyse Crystal structure of the exocytosis-sensitive phosphoprotein, PP63/PARAFUSIN… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KFI
- Type
- protein
- Length
- 1,140 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglucomutase 1
- EC
- 5.4.2.2
- UniProt
- P47244
- Ligands
- ZN, SO4
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphoglucomutase 1 (EC 5.4.2.2) | protein | 570 | 36% helix, 24% strand | P47244 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.77 | 0.80 | 85 | ZN, SO4 |
| 2 | 722 | 0.76 | 0.81 | 84 | SO4 |
| 3 | 636 | 0.74 | 0.81 | 74 | empty |
| 4 | 437 | 0.68 | 0.80 | 46 | empty |
| 5 | 104 | 0.62 | 0.88 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1146 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1KFI · Crystal Structure of the Exocytosis-Sensitive Phosphoprotein, pp63/Parafusin… · the same entry in another collection · chain A against A, TM-score 1.00
- P47244 · AlphaFold monomer V2.0 prediction for phosphoglucomutase-1 (P47244) · 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 P47244
- Elsewhere: RCSB PDB 1KFI · PDBe 1KFI · UniProt P47244
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