MolNFT v1 · #94799 · protein
Crystal structure of the bacillus stearothermophilus phosphofructokinase mutant D12A in complex with pep
4I7E · 6-phosphofructokinase: “Crystal structure of the bacillus stearothermophilus phosphofructokinase mutant D12A in complex with pep”. X-ray diffraction, 1 ligand (PEP), 15 pockets (best druggability 0.84). MolNFT v1 #94799 on…
- PDB
- 4I7E
- Type
- protein
- Length
- 1,276 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphofructokinase
- EC
- 2.7.1.11
- UniProt
- P00512
- Ligands
- PEP
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 6-phosphofructokinase (EC 2.7.1.11) | protein | 319 | 44% helix, 20% strand | P00512 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.84 | 0.86 | 83 | empty |
| 2 | 200 | 0.83 | 0.96 | 30 | empty |
| 3 | 156 | 0.80 | 0.95 | 28 | empty |
| 4 | 705 | 0.72 | 0.79 | 71 | PEP |
| 5 | 686 | 0.70 | 0.78 | 66 | PEP |
Interfaces
6 interfaces between chains.
- C–D · 2297 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2277 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1258 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1163 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 87 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4I7E · Crystal Structure of the Bacillus stearothermophilus Phosphofructokinase Mutant D12A in… · the same entry in another collection · chain A against A, TM-score 1.00
- P00512 · AlphaFold monomer V2.0 prediction for ATP-dependent 6-phosphofructokinase (P00512) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P00512
- Elsewhere: RCSB PDB 4I7E · PDBe 4I7E · UniProt P00512
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