MolNFT v1 · #151102 · protein
R49A variant of beta-phosphoglucomutase from lactococcus lactis complexed with magnesium trifluoride and beta-G6P to 1.3 a.
6HDM: “R49A variant of beta-phosphoglucomutase from lactococcus lactis complexed with magnesium trifluoride and…”. X-ray diffraction, 4 ligands (MGF, BG6, MG), 2 pockets (best druggability 0.70). MolNFT v1 #151102 on GenesisL1: 3D…
- PDB
- 6HDM
- Type
- protein
- Length
- 219 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-phosphoglucomutase
- EC
- 5.4.2.6
- UniProt
- P71447
- Ligands
- MGF, BG6, MG, NA
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-phosphoglucomutase (EC 5.4.2.6) | protein | 219 | 49% helix, 11% strand | P71447 |
Ligands and binding sites
- MGF · Trifluoromagnesate · ligand · chains A
- BG6 · 6-O-phosphono-beta-D-glucopyranose · sugar · chains A
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- PDO · 1,3-propandiol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.70 | 0.93 | 27 | MG, MGF, BG6 |
| 2 | 126 | 0.44 | 0.77 | 20 | PDO, EDO |
Compared structures
- 6HDM · R49A variant of beta-phosphoglucomutase from Lactococcus lactis complexed with magnesium… · the same entry in another collection · chain A against A, TM-score 1.00
- P71447 · AlphaFold monomer V2.0 prediction for beta-phosphoglucomutase (P71447) · 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 P71447
- Elsewhere: RCSB PDB 6HDM · PDBe 6HDM · UniProt P71447
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