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Crystal structure of the phosphofructokinase-2 from escherichia COLI in complex with substrates and products
Analyse Crystal structure of the phosphofructokinase-2 from escherichia COLI in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UQD
- Type
- protein
- Length
- 1,234 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphofructokinase isozyme 2
- EC
- 2.7.1.11
- UniProt
- P06999
- Ligands
- ATP, F6P, FBP, ADP, MG
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | 6-phosphofructokinase isozyme 2 (EC 2.7.1.11) | protein | 309 | 39% helix, 24% strand | P06999 |
| C | 6-phosphofructokinase isozyme 2 (EC 2.7.1.11) | protein | 307 | 39% helix, 24% strand | P06999 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- F6P · 6-O-phosphono-beta-D-fructofuranose · ligand · 2 copies · chains A, C, B, D
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 2 copies · chains B, D, A, C
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B, C
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.81 | 0.83 | 121 | ATP, F6P, MG, FBP, ADP |
| 2 | 552 | 0.76 | 0.84 | 75 | ATP, F6P, MG |
| 3 | 506 | 0.72 | 0.82 | 57 | FBP, ADP, MG |
| 4 | 590 | 0.71 | 0.79 | 38 | empty |
| 5 | 403 | 0.70 | 0.81 | 39 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1297 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1285 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1040 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 952 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 85 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3UQD · Crystal structure of the Phosphofructokinase-2 from Escherichia coli in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P06999 · AlphaFold monomer V2.0 prediction for ATP-dependent 6-phosphofructokinase isozyme 2… · 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 P06999
- Elsewhere: RCSB PDB 3UQD · PDBe 3UQD · UniProt P06999
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