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Structure of baltic herring (clupea harengus) phosphoglucomutase 5 (PGM5) with bound glucose-1-phosphate
Analyse Structure of baltic herring (clupea harengus) phosphoglucomutase 5 (PGM5) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y8Y
- Type
- protein
- Length
- 572 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglucomutase 5
- Ligands
- G1P, NA, NI, CA
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglucomutase 5 | protein | 572 | 36% helix, 26% strand | — |
Ligands and binding sites
- G1P · 1-O-phosphono-alpha-D-glucopyranose · ligand · chains A
- NA · Sodium ion · metal · 5 copies · chains A
- NI · Nickel (II) ion · metal · chains A
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 6 copies · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.72 | 0.87 | 44 | G1P, GOL, NA |
| 2 | 309 | 0.53 | 0.75 | 43 | empty |
| 3 | 58 | 0.48 | 0.85 | 18 | empty |
| 4 | 116 | 0.45 | 0.78 | 23 | GOL |
| 5 | 71 | 0.29 | 0.74 | 15 | empty |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6Y8Y · Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5) with bound… · 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
- Elsewhere: RCSB PDB 6Y8Y · PDBe 6Y8Y
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