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)

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)

wwPDB Validation 3D Report Full Report

Validation slider image for 3IA8

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/prot.22944
Primary Citation Related Structures:
3IA8

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WY91
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-07-28

Deposition Author(s):

Bianchetti, C.M.

Phillips Jr., G.N.

Center for Eukaryotic Structural Genomics (CESG)

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.