3IA8 | pdb_00003ia8

The structure of the C-terminal heme nitrobindin domain of THAP domain-containing protein 4 from Homo sapiens

• PDB DOI: https://doi.org/10.2210/pdb3IA8/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-13 Released: 2009-07-28 
• Deposition Author(s): Bianchetti, C.M., Bingman, C.A., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.201 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Structure of the C-terminal heme-binding domain of THAP domain containing protein 4 from Homo sapiens.

Bianchetti, C.M., Bingman, C.A., Phillips, G.N.

(2011) Proteins 79: 1337-1341

• PubMed: 21387410 
• DOI: https://doi.org/10.1002/prot.22944
• Primary Citation of Related Structures:  
  3IA8

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Organizational Affiliation: 

Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.58 kDa 
• Atom Count: 2,993 
• Modelled Residue Count: 324 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THAP domain-containing protein 4	A, B	163	Homo sapiens	Mutation(s): 0  Gene Names: THAP4, CGI-36, PP238 EC: 5.99
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WY91 (Homo sapiens) Explore Q8WY91  Go to UniProtKB:  Q8WY91
PHAROS:  Q8WY91 GTEx:  ENSG00000176946

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.201 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.933	α = 90
b = 74.694	β = 90
c = 103.064	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-28 
Deposition Author(s): Bianchetti, C.M., Bingman, C.A., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2009-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary