Research workbench
Crystal structure of phosphoserine phosphatase in complex with 3- phosphoglyceric acid from entamoeba histolytica
Analyse Crystal structure of phosphoserine phosphatase in complex with 3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M1X
- Type
- protein
- Length
- 782 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate mutase family protein
- UniProt
- C4M5P9
- Ligands
- 3PG, PO4
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphoglycerate mutase family protein | protein | 197 | 43% helix, 19% strand | C4M5P9 |
| C | Phosphoglycerate mutase family protein | protein | 196 | 43% helix, 19% strand | C4M5P9 |
| D | Phosphoglycerate mutase family protein | protein | 192 | 44% helix, 18% strand | C4M5P9 |
Ligands and binding sites
- 3PG · 3-phosphoglyceric acid · ligand · 2 copies · chains C, D
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.63 | 0.79 | 42 | PO4 |
| 2 | 291 | 0.62 | 0.79 | 30 | PO4 |
| 3 | 223 | 0.59 | 0.80 | 27 | 3PG |
| 4 | 230 | 0.56 | 0.78 | 29 | 3PG |
| 5 | 264 | 0.54 | 0.76 | 31 | empty |
Interfaces
2 interfaces between chains.
- A–B · 886 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 308 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6M1X · Crystal structure of Phosphoserine Phosphatase in complex with 3-Phosphoglyceric Acid… · 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 C4M5P9
- Elsewhere: RCSB PDB 6M1X · PDBe 6M1X · UniProt C4M5P9
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