2A98 | pdb_00002a98

Crystal structure of the catalytic domain of human inositol 1,4,5-trisphosphate 3-kinase C

PDB DOI: https://doi.org/10.2210/pdb2A98/pdb

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

Deposited: 2005-07-11 Released: 2005-07-19
Deposition Author(s): Hallberg, B.M., Ogg, D., Ehn, M., Graslund, S., Hammarstrom, M., Kotenyova, T., Nilsson-Ehle, P., Nordlund, P., Persson, C., Sagemark, J., Schuler, H., Stenmark, P., Thorsell, A.-G., Arrowsmith, C., Edwards, A., Sundstrom, M., Weigelt, J., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.262 (Depositor), 0.253 (DCC)
R-Value Work:
0.218 (Depositor), 0.208 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The crystal structure of the catalytic domain of human inositol 1,4,5-trisphosphate 3-kinase C

Hallberg, B.M., Ogg, D., Arrowsmith, C., Edwards, A., Ehn, M., Graslund, S., Hammarstrom, M., Kotenyova, T., Nilsson-Ehle, P., Nordlund, P., Persson, C., Sagemark, J., Schuler, H., Stenmark, P., Thorsell, A.-G., Sundstrom, M., Weigelt, J.

To be published.

Macromolecule Content

Total Structure Weight: 30.06 kDa
Atom Count: 2,099
Modeled Residue Count: 259
Deposited Residue Count: 259
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol 1,4,5-trisphosphate 3-kinase C	A	259	Homo sapiens	Mutation(s): 0 EC: 2.7.1.127
UniProt & NIH Common Fund Data Resources
Find proteins for Q96DU7 (Homo sapiens) Explore Q96DU7 Go to UniProtKB: Q96DU7
PHAROS: Q96DU7 GTEx: ENSG00000086544
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96DU7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
I3P Query on I3P Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE C₆ H₁₅ O₁₅ P₃ MMWCIQZXVOZEGG-XJTPDSDZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.262 (Depositor), 0.253 (DCC)
R-Value Work: 0.218 (Depositor), 0.208 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.72	α = 90
b = 87.72	β = 90
c = 174.94	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-07-19

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2005-07-19
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description