4D4L

human PFKFB3 in complex with a pyrrolopyrimidone compound

• PDB DOI: https://doi.org/10.2210/pdb4D4L/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-10-29 Released: 2016-01-20 
• Deposition Author(s): Stgallay, S.A., Bennett, N., Critchlow, S., Davies, G., Debreczeni, J.E., Evans, N., Holdgate, G., Jones, N.P., Leach, L., Maman, S., McLoughlin, S., Preston, M., Rigoreau, L., Thomas, A., Walker, G., Walsch, J., Ward, R.A., Wheatley, E., Winter, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.16 Å
• R-Value Free: 0.219 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 52.83 kDa 
• Atom Count: 3,592 
• Modelled Residue Count: 442 
• Deposited Residue Count: 449 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE 3	A	449	Homo sapiens	Mutation(s): 0  EC: 2.7.1.105 (PDB Primary Data), 3.1.3.46 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q16875 (Homo sapiens) Explore Q16875  Go to UniProtKB:  Q16875
PHAROS:  Q16875 GTEx:  ENSG00000170525

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BKS	E [auth A]	5-(4-chlorophenyl)-7-phenyl-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one C18 H12 Cl N3 O VUHYRUNDSUZARS-UHFFFAOYSA-N
F6P	D [auth A]	6-O-phosphono-beta-D-fructofuranose C6 H13 O9 P BGWGXPAPYGQALX-ARQDHWQXSA-N
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
PHS	B [auth A]	PHOSPHONIC ACID H3 O3 P ABLZXFCXXLZCGV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.16 Å
• R-Value Free: 0.219 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.28	α = 90
b = 102.28	β = 90
c = 256.89	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Stgallay, S.A., Bennett, N., Critchlow, S., Davies, G., Debreczeni, J.E., Evans, N., Holdgate, G., Jones, N.P., Leach, L., Maman, S., McLoughlin, S., Preston, M., Rigoreau, L., Thomas, A., Walker, G., Walsch, J., Ward, R.A., Wheatley, E., Winter, J.

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary