MolNFT v2 · #229240 · protein
Crystal Structure Pyrophosphate-fructose 6-phosphate 1-phosphotransferase 1 (Pfk1) from Trichomonas vaginalis (AMP/beta-D-Glucose-6-phosphate complex)
9MED · Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1: “Crystal Structure Pyrophosphate-fructose 6-phosphate 1-phosphotransferase 1 (Pfk1) from Trichomonas vaginalis…”. X-ray diffraction at 2.62, 6 ligands (AMP, PPV, BG6), 19…
- PDB
- 9MED
- Type
- protein
- Length
- 1,680 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.62
- Source
- Trichomonas vaginalis G3
- Molecule
- Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1
- EC
- 2.7.1.90
- UniProt
- O61068
- Ligands
- AMP, PPV, BG6, MG, PO4, CL
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.62 · 3 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1 (EC 2.7.1.90) | protein | 417 | 49% helix, 18% strand | O61068 |
| B, C | Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1 (EC 2.7.1.90) | protein | 423 | 48% helix, 17% strand | O61068 |
| D | Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1 (EC 2.7.1.90) | protein | 417 | 48% helix, 17% strand | O61068 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, C, B, D
- PPV · Pyrophosphate · ligand · chains A
- BG6 · 6-O-phosphono-beta-D-glucopyranose · sugar · 2 copies · chains B, D, A, C
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · 9 copies · chains A, D, B, C
- CL · Chloride ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.83 | 0.88 | 62 | empty |
| 2 | 531 | 0.83 | 0.89 | 66 | empty |
| 3 | 698 | 0.83 | 0.87 | 65 | empty |
| 4 | 1040 | 0.81 | 0.83 | 128 | PO4 |
| 5 | 1082 | 0.81 | 0.83 | 123 | PPV, PO4, MG |
Interfaces
6 interfaces between chains.
- B–D · 2417 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 2415 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1396 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1381 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 47 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- O61068 · AlphaFold monomer V2.0 prediction for pyrophosphate--fructose 6-phosphate… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O61068
- Elsewhere: RCSB PDB 9MED · PDBe 9MED · UniProt O61068
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