Research workbench
R-state AMP complex reveals initial steps of the quaternary transition of fructose-1,6-bisphosphatase
Analyse R-state AMP complex reveals initial steps of the quaternary transition of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YZ0
- Type
- protein
- Length
- 658 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructose-1,6-bisphosphatase
- EC
- 3.1.3.11
- UniProt
- P00636
- Ligands
- F6P, AMP, MG
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fructose-1,6-bisphosphatase (EC 3.1.3.11) | protein | 329 | 39% helix, 23% strand | P00636 |
Ligands and binding sites
- F6P · 6-O-phosphono-beta-D-fructofuranose · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.72 | 0.77 | 77 | F6P |
| 2 | 324 | 0.64 | 0.80 | 39 | empty |
| 3 | 211 | 0.57 | 0.80 | 40 | F6P |
| 4 | 134 | 0.51 | 0.80 | 22 | empty |
| 5 | 141 | 0.48 | 0.78 | 29 | AMP |
Interfaces
1 interface between chains.
- A–B · 2278 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 1YZ0 · R-State AMP Complex Reveals Initial Steps of the Quaternary Transition of… · the same entry in another collection · chain A against A, TM-score 1.00
- P00636 · AlphaFold monomer V2.0 prediction for fructose-1,6-bisphosphatase 1 (P00636) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P00636
- Elsewhere: RCSB PDB 1YZ0 · PDBe 1YZ0 · UniProt P00636
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