4L1J | pdb_00004l1j

Three dimensional structure of mutant D143A of human HD domain-containing protein 2, Northeast Structural Genomics Consortium (NESG) Target HR6723

• PDB DOI: https://doi.org/10.2210/pdb4L1J/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-06-03 Released: 2013-06-19 
• Deposition Author(s): Kuzin, A., Su, M., Yakunin, A., Beloglazova, O., Seetharaman, J., Maglaqui, M., Xiao, R., Lee, D., Brown, G., Flick, R., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.201 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Three dimensional structure of mutant D143A of human HD domain-containing protein 2, Northeast Structural Genomics Consortium (NESG) Target HR6723

Kuzin, A., Su, M., Yakunin, A., Beloglazova, O., Seetharaman, J., Maglaqui, M., Xiao, R., Lee, D., Brown, G., Flick, R., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.58 kDa 
• Atom Count: 3,441 
• Modeled Residue Count: 383 
• Deposited Residue Count: 408 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HD domain-containing protein 2	A	204	Homo sapiens	Mutation(s): 1  EC: 3.1.3.89
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z4H3 (Homo sapiens) Explore Q7Z4H3  Go to UniProtKB:  Q7Z4H3
PHAROS:  Q7Z4H3 GTEx:  ENSG00000111906

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HD domain-containing protein 2 (Phosphorylate)	B	204	Homo sapiens	Mutation(s): 1  EC: 3.1.3.89
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z4H3 (Homo sapiens) Explore Q7Z4H3  Go to UniProtKB:  Q7Z4H3
PHAROS:  Q7Z4H3 GTEx:  ENSG00000111906

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE4	I [auth B]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C16 H34 O8 PJWQOENWHPEPKI-UHFFFAOYSA-N
PEG	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
SEP	B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.201 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.991	α = 90
b = 69.929	β = 90
c = 105.778	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-19 
Deposition Author(s): Kuzin, A., Su, M., Yakunin, A., Beloglazova, O., Seetharaman, J., Maglaqui, M., Xiao, R., Lee, D., Brown, G., Flick, R., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2013-06-19
  Type: Initial release
  
• Version 1.1: 2013-12-25
  Changes: Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-10-16
  Changes: Structure summary