2YBX

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free: 0.238
R-Value Work: 0.188
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 90.72 kDa
Atom Count: 5,362
Modelled Residue Count: 634
Deposited Residue Count: 788
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48426
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PHD Query on 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
R-Value Work: 0.188
R-Value Observed: 0.191
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-01-25

Deposition Author(s):

Revision History (Full details and data files)

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

Prepare Data

Validate Data

Deposit Data

Help and Resources

2YBX

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)