2YBX | pdb_00002ybx

Crystal Structure of Human Phosphatidylinositol-5-phosphate 4-kinase type-2 alpha

• PDB DOI: https://doi.org/10.2210/pdb2YBX/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-03-30 Released: 2012-01-25 
• Deposition Author(s): Tresaugues, L., Moche, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Ekblad, T., Flodin, S., Graslund, S., Karlberg, T., Kotenyova, T., Kouznetsova, E., Nyman, T., Persson, C., Schuler, H., Siponen, M.I., Thorsell, A.G., Wahlberg, E., Weigelt, J., Nordlund, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 
  0.238 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human Phosphatidylinositol-5-Phosphate 4-Kinase Type-2 Alpha

Tresaugues, L., Moche, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Ekblad, T., Flodin, S., Graslund, S., Karlberg, T., Kotenyova, T., Kouznetsova, E., Nyman, T., Persson, C., Schuler, H., Siponen, M.I., Thorsell, A.G., Wahlberg, E., Weigelt, J., Nordlund, P.

To be published.

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: 90.72 kDa 
• Atom Count: 5,362 
• Modeled Residue Count: 634 
• Deposited Residue Count: 788 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHATIDYLINOSITOL-5-PHOSPHATE 4-KINASE TYPE-2 ALPHA	A, B	394	Homo sapiens	Mutation(s): 0  EC: 2.7.1.149
UniProt & NIH Common Fund Data Resources
Find proteins for P48426 (Homo sapiens) Explore P48426  Go to UniProtKB:  P48426
PHAROS:  P48426 GTEx:  ENSG00000150867

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PHD	A, B	L-PEPTIDE LINKING	C4 H8 N O7 P		ASP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free:  0.238 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.04	α = 90
b = 98.508	β = 93.43
c = 104.879	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-25 
Deposition Author(s): Tresaugues, L., Moche, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Ekblad, T., Flodin, S., Graslund, S., Karlberg, T., Kotenyova, T., Kouznetsova, E., Nyman, T., Persson, C., Schuler, H., Siponen, M.I., Thorsell, A.G., Wahlberg, E., Weigelt, J., Nordlund, P.

Revision History  

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description