4H46

Crystal Structure of AMP complexes of NEM modified Porcine Liver Fructose-1,6-bisphosphatase

• PDB DOI: https://doi.org/10.2210/pdb4H46/pdb

• Classification: HYDROLASE
• Organism(s): Sus scrofa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-09-16 Released: 2013-09-18 
• Deposition Author(s): Gao, Y., Honzatko, R.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.256 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

Fluorescent 2',3'-O-(2,4,6-trinitrophenyl) (TNP)-AMP Is an Active Site Inhibitor for Porcine Liver Fructose-1,6-bisphosphatase Rather Than Allosteric Inhibitor

Gao, Y., Honzatko, R.B.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.54 kDa 
• Atom Count: 2,594 
• Modelled Residue Count: 319 
• Deposited Residue Count: 337 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-1,6-bisphosphatase 1	A	337	Sus scrofa	Mutation(s): 0  Gene Names: FBP, FBP1 EC: 3.1.3.11
UniProt
Find proteins for P00636 (Sus scrofa) Explore P00636  Go to UniProtKB:  P00636

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	E [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
F6P	B [auth A]	6-O-phosphono-beta-D-fructofuranose C6 H13 O9 P BGWGXPAPYGQALX-ARQDHWQXSA-N
NEN	F [auth A]	1-ETHYL-PYRROLIDINE-2,5-DIONE C6 H9 N O2 GHAZCVNUKKZTLG-UHFFFAOYSA-N
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.256 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.561	α = 90
b = 78.673	β = 90
c = 164.928	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-18 
Deposition Author(s): Gao, Y., Honzatko, R.B.

Revision History  

• Version 1.0: 2013-09-18
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-10-09
  Changes: Structure summary