2HHL

Crystal structure of the human small CTD phosphatase 3 isoform 1

• PDB DOI:  https://doi.org/10.2210/pdb2HHL/pdb

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


• Deposited: 2006-06-28 Released: 2006-08-29 
• Deposition Author(s): Malashkevich, V.N., Toro, R., Ramagopal, U., Sauder, J.M., Schwinn, K.D., Thompson, D.A., Rutter, M.E., Dickey, M., Groshong, C., Bain, K.T., Adams, J.M., Reyes, C., Rooney, I., Powell, A., Boice, A., Gheyi, T., Ozyurt, S., Atwell, S., Wasserman, S.R., Emtage, S., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.252 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Literature

Structural genomics of protein phosphatases.

Almo, S.C., Bonanno, J.B., Sauder, J.M., Emtage, S., Dilorenzo, T.P., Malashkevich, V., Wasserman, S.R., Swaminathan, S., Eswaramoorthy, S., Agarwal, R., Kumaran, D., Madegowda, M., Ragumani, S., Patskovsky, Y., Alvarado, J., Ramagopal, U.A., Faber-Barata, J., Chance, M.R., Sali, A., Fiser, A., Zhang, Z.Y., Lawrence, D.S., Burley, S.K.

(2007) J Struct Funct Genomics 8: 121-140

• PubMed: 18058037 
• DOI: https://doi.org/10.1007/s10969-007-9036-1
• Primary Citation of Related Structures:  
  1RXD, 2FH7, 2G59, 2HCM, 2HHL, 2HXP, 2HY3, 2I0O, 2I1Y, 2I44, 2IQ1, 2IRM, 2ISN, 2NV5, 2OYC, 2P27, 2P4U, 2P69, 2P8E, 2PBN, 2Q5E, 2QJC, 2R0B


• PubMed Abstract: 
  

The New York SGX Research Center for Structural Genomics (NYSGXRC) of the NIGMS Protein Structure Initiative (PSI) has applied its high-throughput X-ray crystallographic structure determination platform to systematic studies of all human protein phosphatases and protein phosphatases from biomedically-relevant pathogens. To date, the NYSGXRC has determined structures of 21 distinct protein phosphatases: 14 from human, 2 from mouse, 2 from the pathogen Toxoplasma gondii, 1 from Trypanosoma brucei, the parasite responsible for African sleeping sickness, and 2 from the principal mosquito vector of malaria in Africa, Anopheles gambiae. These structures provide insights into both normal and pathophysiologic processes, including transcriptional regulation, regulation of major signaling pathways, neural development, and type 1 diabetes. In conjunction with the contributions of other international structural genomics consortia, these efforts promise to provide an unprecedented database and materials repository for structure-guided experimental and computational discovery of inhibitors for all classes of protein phosphatases.

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Organizational Affiliation: 

Albert Einstein College of Medicine, Bronx, NY, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 98.33 kDa 
• Atom Count: 6,472 
• Modelled Residue Count: 715 
• Deposited Residue Count: 780 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CTD small phosphatase-like protein	A, B, C, D	195	Homo sapiens	Mutation(s): 0  Gene Names: CTDSPL, C3orf8, NIF1, NIFL, YA22, SCP3 EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for O15194 (Homo sapiens) Explore O15194  Go to UniProtKB:  O15194
PHAROS:  O15194

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KEG	E [auth A], F [auth C], G [auth D]	12-TUNGSTOPHOSPHATE O40 P W12 WLQKSSFZMDTTCM-YEFKIAJVAA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.252 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.419	α = 90
b = 49.857	β = 96.9
c = 179.747	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-29 
Deposition Author(s): Malashkevich, V.N., Toro, R., Ramagopal, U., Sauder, J.M., Schwinn, K.D., Thompson, D.A., Rutter, M.E., Dickey, M., Groshong, C., Bain, K.T., Adams, J.M., Reyes, C., Rooney, I., Powell, A., Boice, A., Gheyi, T., Ozyurt, S., Atwell, S., Wasserman, S.R., Emtage, S., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2006-08-29
  Type: Initial release
  
• Version 1.1: 2008-03-20
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.5: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2023-08-30
  Changes: Data collection, Database references, Refinement description