Research workbench
Binding driven structural changes in crystaline phosphoglucomutase associated with chemical reaction
Analyse Binding driven structural changes in crystaline phosphoglucomutase associated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1C47
- Type
- protein
- Length
- 1,122 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-D-glucose 1,6-bisphosphate phosphotransferase
- EC
- 2.7.5.1
- UniProt
- P00949
- Ligands
- G16, CD
- Pockets
- 17 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-D-glucose 1,6-bisphosphate phosphotransferase (EC 2.7.5.1) | protein | 561 | 36% helix, 26% strand | P00949 |
Ligands and binding sites
- G16 · 1,6-di-O-phosphono-alpha-D-glucopyranose · ligand · chains A
- CD · Cadmium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.66 | 0.77 | 48 | empty |
| 2 | 383 | 0.62 | 0.78 | 43 | G16 |
| 3 | 301 | 0.60 | 0.78 | 29 | empty |
| 4 | 218 | 0.54 | 0.77 | 24 | empty |
| 5 | 67 | 0.50 | 0.85 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 622 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1C47 · Binding driven structural changes in crystaline phosphoglucomutase associated with… · the same entry in another collection · chain A against A, TM-score 1.00
- P00949 · AlphaFold monomer V2.0 prediction for phosphoglucomutase-1 (P00949) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P00949
- Elsewhere: RCSB PDB 1C47 · PDBe 1C47 · UniProt P00949
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