3IHY | pdb_00003ihy

Human PIK3C3 crystal structure

PDB DOI: https://doi.org/10.2210/pdb3IHY/pdb

Deposited: 2009-07-31 Released: 2009-10-13
Deposition Author(s): Siponen, M.I., Tresaugues, L., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Kotzsch, A., Kragh Nielsen, T., Moche, M., Nyman, T., Persson, C., Roos, A.K., Sagemark, J., Schueler, H., Schutz, P., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Nordlund, P., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.255 (Depositor), 0.234 (DCC)
R-Value Work:
0.187 (Depositor)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3IHY

This is version 1.3 of the entry. See complete history.

Literature

Human PIK3C3 crystal structure

Siponen, M.I., Tresaugues, L., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Kotzsch, A., Kragh Nielsen, T., Moche, M., Nyman, T., Persson, C., Roos, A.K., Sagemark, J., Schueler, H., Schutz, P., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Nordlund, P.

To be published.

Macromolecule Content

Total Structure Weight: 342.78 kDa
Atom Count: 21,670
Modeled Residue Count: 2,674
Deposited Residue Count: 3,000
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3-kinase catalytic subunit type 3	A, B, C, D, E	600	Homo sapiens	Mutation(s): 0 Gene Names: PIK3C3, PIK3C3A 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NEB9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.255 (Depositor), 0.234 (DCC)
R-Value Work: 0.187 (Depositor)
R-Value Observed: 0.190 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.297	α = 107.77
b = 96.491	β = 91.75
c = 150.679	γ = 92.41

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-10-13

Deposition Author(s):

Arrowsmith, C.H.

Hammarstrom, M.

Kragh Nielsen, T.

Van Den Berg, S.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2009-10-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2024-02-21
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.