MolNFT v1 · #23529 · protein
Crystal structure of a hypothetical ADP-dependent phosphofructokinase from pyrococcus horikoshii OT3
1U2X · ADP-specific phosphofructokinase: “Crystal structure of a hypothetical ADP-dependent phosphofructokinase from pyrococcus horikoshii OT3”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.69). MolNFT v1 #23529 on…
- PDB
- 1U2X
- Type
- protein
- Length
- 900 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-specific phosphofructokinase
- EC
- 2.7.1.146
- UniProt
- O59355
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ADP-specific phosphofructokinase (EC 2.7.1.146) | protein | 450 | 46% helix, 22% strand | O59355 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.69 | 0.77 | 61 | empty |
| 2 | 610 | 0.68 | 0.77 | 62 | empty |
| 3 | 565 | 0.68 | 0.77 | 67 | SO4 |
| 4 | 580 | 0.66 | 0.77 | 67 | SO4 |
| 5 | 75 | 0.41 | 0.79 | 16 | SO4 |
Interfaces
1 interface between chains.
- A–B · 911 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 1U2X · Crystal Structure of a Hypothetical ADP-dependent Phosphofructokinase from Pyrococcus… · the same entry in another collection · chain A against A, TM-score 1.00
- O59355 · AlphaFold monomer V2.0 prediction for ADP-specific phosphofructokinase (O59355) · a predicted model of the same protein · 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 O59355
- Elsewhere: RCSB PDB 1U2X · PDBe 1U2X · UniProt O59355
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