3LS8 | pdb_00003ls8

Crystal structure of human PIK3C3 in complex with 3-[4-(4-Morpholinyl)thieno[3,2-d]pyrimidin-2-yl]-phenol

• PDB DOI: https://doi.org/10.2210/pdb3LS8/pdb

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


• Deposited: 2010-02-12 Released: 2010-03-23 
• Deposition Author(s): Tresaugues, L., Welin, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kotenyova, T., Kraulis, P., Moche, M., Nyman, T., Persson, C., Schuler, H., Schutz, P., Siponen, M.I., Thorsell, A.G., Van den Berg, S., Wahlberg, E., Weigelt, J., Wisniewska, M., Nordlund, P., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.251 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human PIK3C3 in complex with 3-[4-(4-Morpholinyl)thieno[3,2-d]pyrimidin-2-yl]-phenol

Tresaugues, L., Welin, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kotenyova, T., Kraulis, P., Moche, M., Nyman, T., Persson, C., Schuler, H., Schutz, P., Siponen, M.I., Thorsell, A.G., Van den Berg, S., Wahlberg, E., Weigelt, J., Wisniewska, M., Nordlund, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 141.1 kDa 
• Atom Count: 9,027 
• Modeled Residue Count: 1,069 
• Deposited Residue Count: 1,228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3-kinase catalytic subunit type 3	A, B	614	Homo sapiens	Mutation(s): 0  Gene Names: PIK3C3 EC: 2.7.1.137
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NEB9 (Homo sapiens) Explore Q8NEB9  Go to UniProtKB:  Q8NEB9
PHAROS:  Q8NEB9 GTEx:  ENSG00000078142

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AJZ	C [auth A], G [auth B]	3-(4-morpholin-4-ylthieno[3,2-d]pyrimidin-2-yl)phenol C16 H15 N3 O2 S XXLAEKOWCYJOKK-UHFFFAOYSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth A], E [auth A], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.251 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.686	α = 90
b = 141.151	β = 90
c = 163.975	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-23 
Deposition Author(s): Tresaugues, L., Welin, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kotenyova, T., Kraulis, P., Moche, M., Nyman, T., Persson, C., Schuler, H., Schutz, P., Siponen, M.I., Thorsell, A.G., Van den Berg, S., Wahlberg, E., Weigelt, J., Wisniewska, M., Nordlund, P., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-03-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description