Research workbench
Structure of baltic herring (clupea harengus) phosphoglucomutase 5 (PGM5)
Analyse Structure of baltic herring (clupea harengus) phosphoglucomutase 5 (PGM5) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y8Z
- Type
- protein
- Length
- 567 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglucomutase 5
- Ligands
- NA, NI, CA
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglucomutase 5 | protein | 567 | 37% helix, 26% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A
- NI · Nickel (II) ion · metal · chains A
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 4 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 682 | 0.69 | 0.77 | 66 | NA, GOL |
| 2 | 121 | 0.45 | 0.78 | 22 | empty |
| 3 | 72 | 0.30 | 0.74 | 15 | empty |
| 4 | 63 | 0.29 | 0.74 | 24 | empty |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6Y8Z · Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5) · 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 6Y8Z · PDBe 6Y8Z
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