Research workbench
Streptococcus pyogenes phosphoglycerol transferase gach in complex with sn-glycerol-1-phosphate
Analyse Streptococcus pyogenes phosphoglycerol transferase gach in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DGM
- Type
- protein
- Length
- 763 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerol transferase gach
- UniProt
- Q9A0F9
- Ligands
- 1GP, MN, CA
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglycerol transferase gach | protein | 381 | 43% helix, 16% strand | Q9A0F9 |
| B | Phosphoglycerol transferase gach | protein | 382 | 43% helix, 16% strand | Q9A0F9 |
Ligands and binding sites
- 1GP · Sn-glycerol-1-phosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 662 | 0.72 | 0.79 | 89 | 1GP |
| 2 | 74 | 0.40 | 0.79 | 19 | empty |
| 3 | 104 | 0.38 | 0.75 | 22 | empty |
| 4 | 61 | 0.38 | 0.79 | 18 | empty |
| 5 | 88 | 0.36 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1020 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6DGM · Streptococcus pyogenes phosphoglycerol transferase GacH in complex with… · 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 Q9A0F9
- Elsewhere: RCSB PDB 6DGM · PDBe 6DGM · UniProt Q9A0F9
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