MolNFT v1 · #81305 · protein
Crystal structure of the phosphofructokinase-2 from escherichia COLI in complex with cesium and ATP
3UMP · 6-phosphofructokinase isozyme 2: “Crystal structure of the phosphofructokinase-2 from escherichia COLI in complex with cesium and ATP”. X-ray diffraction, 3 ligands (ATP, MG, CS), 3 pockets (best druggability 0.77). MolNFT v1 #81305…
- PDB
- 3UMP
- Type
- protein
- Length
- 617 residues
- Chains
- 2
- 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, MG, CS
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-phosphofructokinase isozyme 2 (EC 2.7.1.11) | protein | 309 | 39% helix, 22% strand | P06999 |
| B | 6-phosphofructokinase isozyme 2 (EC 2.7.1.11) | protein | 308 | 38% helix, 22% strand | P06999 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CS · Cesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 769 | 0.77 | 0.82 | 71 | MG, ATP |
| 2 | 691 | 0.76 | 0.81 | 70 | ATP, MG |
| 3 | 102 | 0.66 | 0.90 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1528 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3UMP · 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 B 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 P06999
- Elsewhere: RCSB PDB 3UMP · PDBe 3UMP · UniProt P06999
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