4L7W | pdb_00004l7w

Crystal structure mutant H77A of human HD domain-containing protein 2, Genomics Consortium (NESG) Target HR6723

• PDB DOI: https://doi.org/10.2210/pdb4L7W/pdb

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


• Deposited: 2013-06-14 Released: 2013-07-03 
• Deposition Author(s): Kuzin, A., Su, M., Yakunin, A., Beloglazova, N., 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: 2.31 Å
• R-Value Free: 
  0.228 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Northeast Structural Genomics Consortium Target HR6723

Kuzin, A., Su, M., Yakunin, A., Beloglazova, N., 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)

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: 23.93 kDa 
• Atom Count: 1,570 
• Modeled Residue Count: 188 
• Deposited Residue Count: 204 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HD domain-containing protein 2	A	204	Homo sapiens	Mutation(s): 1  Gene Names: HDDC2, C6orf74, NS5ATP2, CGI-130 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free:  0.228 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.38	α = 90
b = 71.38	β = 90
c = 199.308	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-03 
Deposition Author(s): Kuzin, A., Su, M., Yakunin, A., Beloglazova, N., 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: 2013-07-03
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-11-20
  Changes: Structure summary