MolNFT v1 · #151098 · protein
R49A variant of beta-phosphoglucomutase from lactococcus lactis in an open conformer to 2.0 a.
6HDI: “R49A variant of beta-phosphoglucomutase from lactococcus lactis in an open conformer to 2.0 a.”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.77). MolNFT v1 #151098 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6HDI
- Type
- protein
- Length
- 441 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-phosphoglucomutase
- EC
- 5.4.2.6
- UniProt
- P71447
- Ligands
- MG
- Pockets
- 1 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-phosphoglucomutase (EC 5.4.2.6) | protein | 220 | 52% helix, 11% strand | P71447 |
| B | Beta-phosphoglucomutase (EC 5.4.2.6) | protein | 221 | 51% helix, 11% strand | P71447 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.77 | 0.79 | 107 | EDO |
Interfaces
1 interface between chains.
- A–B · 596 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6HDI · R49A variant of beta-phosphoglucomutase from Lactococcus lactis in an open conformer to… · 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 B against A, TM-score 0.88
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 6HDI · PDBe 6HDI · UniProt P71447
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