Research workbench
Crystal structure of the R503Q missense variant of human PGM1
Analyse Crystal structure of the R503Q missense variant of human PGM1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VG7
- Type
- protein
- Length
- 1,126 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglucomutase-1
- EC
- 5.4.2.2
- UniProt
- P36871
- Ligands
- MG, SO4
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglucomutase-1 (EC 5.4.2.2) | protein | 564 | 37% helix, 26% strand | P36871 |
| B | Phosphoglucomutase-1 (EC 5.4.2.2) | protein | 562 | 36% helix, 26% strand | P36871 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 18 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.67 | 0.78 | 60 | SO4, GOL |
| 2 | 638 | 0.66 | 0.76 | 65 | SO4, GOL |
| 3 | 619 | 0.66 | 0.76 | 64 | SO4 |
| 4 | 138 | 0.48 | 0.78 | 27 | GOL |
| 5 | 143 | 0.44 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 521 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
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 P36871
- Elsewhere: RCSB PDB 5VG7 · PDBe 5VG7 · UniProt P36871
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