Research workbench
2.27 ångström crystal structure of beta-phosphoglucomutase (pgmb) from clostridium difficile
Analyse 2.27 ångström crystal structure of beta-phosphoglucomutase (pgmb) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GIB
- Type
- protein
- Length
- 448 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-phosphoglucomutase
- EC
- 5.4.2.6
- UniProt
- Q185X7
- Ligands
- GLY, NA, PO4
- Pockets
- 5 · best druggability 0.67
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 | 225 | 50% helix, 11% strand | Q185X7 |
| B | Beta-phosphoglucomutase (EC 5.4.2.6) | protein | 223 | 52% helix, 11% strand | Q185X7 |
Ligands and binding sites
- GLY · Glycine · ligand · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 5 copies · chains A, B
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 | 116 | 0.67 | 0.90 | 33 | PO4 |
| 2 | 183 | 0.62 | 0.83 | 46 | PO4 |
| 3 | 123 | 0.39 | 0.75 | 24 | empty |
| 4 | 55 | 0.35 | 0.79 | 15 | empty |
| 5 | 90 | 0.35 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 733 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4GIB · 2.27 Angstrom Crystal Structure of beta-Phosphoglucomutase (pgmB) from Clostridium… · 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
- Every structure of UniProt Q185X7
- Elsewhere: RCSB PDB 4GIB · PDBe 4GIB · UniProt Q185X7
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