2ODT

Structure of human Inositol 1,3,4-trisphosphate 5/6-kinase

• PDB DOI: https://doi.org/10.2210/pdb2ODT/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-12-26 Released: 2007-02-13 
• Deposition Author(s): Busam, R.D., Arrowsmith, C., Berglund, H., Collins, R., Edwards, A., Ericsson, U.B., Flodin, S., Flores, A., Hammarstrom, M., Holmberg, S.L., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Ogg, D., Sagemark, J., Sundstrom, M., Uppenberg, J., Van Den Berg, S., Weigelt, J., Persson, C., Thorsell, A.G., Hallberg, B.M., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Structure of human Inositol 1,3,4-trisphosphate 5/6-kinase

Busam, R.D., Arrowsmith, C., Berglund, H., Collins, R., Edwards, A., Ericsson, U.B., Flodin, S., Flores, A., Hammarstrom, M., Holmberg, S.L., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Ogg, D., Sagemark, J., Sundstrom, M., Uppenberg, J., Van Den Berg, S., Weigelt, J., Persson, C., Thorsell, A.G., Hallberg, B.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.42 kDa 
• Atom Count: 2,841 
• Modelled Residue Count: 315 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol-tetrakisphosphate 1-kinase	A [auth X]	328	Homo sapiens	Mutation(s): 7  Gene Names: ITPK1 EC: 2.7.1.134 (PDB Primary Data), 2.7.1.159 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13572 (Homo sapiens) Explore Q13572  Go to UniProtKB:  Q13572
PHAROS:  Q13572 GTEx:  ENSG00000100605

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth X]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.33	α = 90
b = 39.55	β = 98.4
c = 67.39	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DNA	data collection
XDS	data reduction
XSCALE	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-13 
Deposition Author(s): Busam, R.D., Arrowsmith, C., Berglund, H., Collins, R., Edwards, A., Ericsson, U.B., Flodin, S., Flores, A., Hammarstrom, M., Holmberg, S.L., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Ogg, D., Sagemark, J., Sundstrom, M., Uppenberg, J., Van Den Berg, S., Weigelt, J., Persson, C., Thorsell, A.G., Hallberg, B.M., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-02-13
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Structure summary