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Crystal structure of a phosphofructokinase from pyrococcus horikoshii OT3 with AMP
Analyse Crystal structure of a phosphofructokinase from pyrococcus horikoshii OT3 with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DRW
- Type
- protein
- Length
- 910 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
- AMP, NA
- Pockets
- 12 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-specific phosphofructokinase (EC 2.7.1.146) | protein | 460 | 44% helix, 20% strand | O59355 |
| B | ADP-specific phosphofructokinase (EC 2.7.1.146) | protein | 450 | 45% helix, 22% strand | O59355 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.65 | 0.77 | 71 | AMP, NA |
| 2 | 361 | 0.59 | 0.76 | 55 | empty |
| 3 | 261 | 0.57 | 0.78 | 30 | empty |
| 4 | 251 | 0.57 | 0.78 | 28 | empty |
| 5 | 145 | 0.53 | 0.80 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1337 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3DRW · Crystal Structure of a Phosphofructokinase from Pyrococcus horikoshii OT3 with AMP · 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 B 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 O59355
- Elsewhere: RCSB PDB 3DRW · PDBe 3DRW · UniProt O59355
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