Percentage of the aligned query length over the whole query sequence
Percentage of the aligned subject sequence over the whole subject sequence
Click to View Superposition
Protein Chain ID(s)
DNA Chain ID(s)
A TF-unit is defined as an entity that (a) the protein is a monomer or there are at least 3 residue-residue contacts (based on heavy atom distance cutoff of 4.5 angstroms) between two protein chains; and (b) there are at least 2 bases in contact with the protein unit.
Number of protein side-chains that are in contact with DNA bases
Sequence identity between bound and unbound TF-chains
Sequence identity between bound and unbound TF-units
Sequence identity between query and homologous bound TF-units
Root-mean-square-distance between the CΑs of bound and unbound TF-chains
Root-mean-square-distance between the CΑs of bound and unbound TF-units
Root-mean-square-distance between the CΑs of query and homologous bound TF-units
Root-mean-square-distance between the CΑs of the DNA-binding regions of bound and unbound TF-chains
Root-mean-square-distance between the CΑs of the whole structures of bound and unbound TF-chains
Root-mean-square-distance between the CΑs of the DNA-binding regions of bound and unbound TF-units
Root-mean-square-distance between the CΑs of the whole structures of bound and unbound TF-units
Root-mean-square-distance between the CΑs of the DNA-binding regions of query and homologous TF-chains
Root-mean-square-distance between the CΑs of the whole structures of query and homologous TF-chains
Binding profiles for eukaryotic transcription factors.
Binding profiles for Escherichia coli transcription factors.
Thermodynatic data for transcription factor-DNA binding
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Transcription Factor-DNA Interaction Data Depository


Transcription Factor
chains A/B: Segmentation polarity homeobox protein engrailed.
Function
TF-DNA Unit
NameChainsNRBC?
3hddu0a,c,d4
3hddu1b,c,d4
SCOP IDs
3hddaa.4.1.1
3hddba.4.1.1
CATH IDs
3hdda1.10.10.60
3hddb1.10.10.60
 


Homologous Unbound TF-Chain(s)
Bound
Chain
Unbound
Chain
Sequence IdentityE-ValueHit?
Coverage
Query?
Coverage
TMScoreRMSD?
3hddb2jwta1001.0e-2696.798.30.8951.29
3hddb1p7jd98.35.0e-2610098.30.9130.66
3hddb1p7jc98.35.0e-2610098.30.8920.54
3hddb1p7jb98.35.0e-2610098.30.8810.47
3hddb1p7ja98.35.0e-2610098.30.8980.84
3hddb1p7id98.35.0e-2610098.30.8921.27
3hddb1p7ic98.35.0e-2610098.30.8760.35
3hddb1p7ib98.35.0e-2610098.30.8690.42
3hddb1p7ia98.35.0e-2610098.30.8870.96
3hdda2jwta1001.0e-2696.798.30.8861.07
3hdda1p7jd98.35.0e-2610098.30.9150.72
3hdda1p7jc98.35.0e-2610098.30.8960.64
3hdda1p7jb98.35.0e-2610098.30.9070.37
3hdda1p7ja98.35.0e-2610098.30.8980.52
3hdda1p7id98.35.0e-2610098.30.9020.83
3hdda1p7ic98.35.0e-2610098.30.8880.38
3hdda1p7ib98.35.0e-2610098.30.8800.46
3hdda1p7ia98.35.0e-2610098.30.8920.74


Homologous Bound TF-Chain(s)
Query
Chain
Homologous
Chain
Sequence
Identity
E-ValueHit?
Coverage
Query?
Coverage
TMScoreRMSD?
3hddb3hdda1001.0e-291001000.9380.42
3hddb1hddd1003.0e-2996.798.30.9810.34
3hddb1hddc1003.0e-2996.798.30.9331.22
3hddb2hddb98.31.0e-2896.798.30.9640.35
3hddb2hdda98.31.0e-2896.798.30.9280.5
3hddb1du0b98.22.0e-27100950.9830.33
3hddb1du0a98.22.0e-27100950.8860.55
3hdda3hddb1001.0e-291001000.9550.42
3hdda1hddd1003.0e-2996.798.30.9530.56
3hdda1hddc1003.0e-2996.798.30.9690.48
3hdda2hddb98.31.0e-2896.798.30.9330.46
3hdda2hdda98.31.0e-2896.798.30.9810.36
3hdda1du0b98.22.0e-27100950.9510.45
3hdda1du0a98.22.0e-27100950.9370.42


Additional DNA Binding Site(s)
SourceBinding SitesPDB Chain IdsName
JasparMA0220.1 en


Thermodynamic Data (ProNIT)
EntriesProtein MutationsDNA Mutations
5943wildwild
5949wildwild
5955wildwild

TFinDit is a database and web service for structural bioinformatics studies of transcription factor (TF)-DNA interactions. Various datasets can be generated based on one or more search options specified by users.

Under "Advanced Search", users can search TFinDit for:
  • Pairs of bound and unbound transcription factor structures
  • Homologous TF-DNA complex structures
  • Annotated binding DNA sequences for TF structures from Jaspar1 and RegulonDB2
  • Thermodynamic wild-type and mutant TF-DNA binding data 3
  • Non-redundant TF-DNA complexes for development purposes

Users can also get detailed information for each entry in TFinDit using “Search by PDB ID”, which includes the number of unbound structures, the number of homologous complex structures, the number of annotated binding sequences in Jaspar and RegulonDB, and the thermodynamic data for wild-type and mutant transcription factor and/or DNA molecules. The “Search by PDB ID” page also provides quick links to other popular database/webservers for each complex.

Update History and Statistics

Date# Bound Chains# Unbound Chains# ProNIT Mappings# Jaspar and RegulonDB Mappings
July 201213912370307433
February 201315713160314433
October 201317163922315433
January 201417374049315556

1Bryne JC et al. JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res. 2008 Jan;36(Database issue):D102-6.
2Socorro Gama-Castro et al. RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res. 2008 Jan; 36 (Database issue):D120-4.
3Kumar MD et al. ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions. Nuleic Acids Res. 2006; 34: D204-6.

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  • 3D-footprint: database of DNA-binding protein structures.1
  • BIPA: a database for protein-nucleic acid interaction.2
  • ccPDB: compilation and creation of datasets from PDB.3
  • DDNA3: DNA binding domain prediction.4
  • NDB: a repository of three-dimensional structural information about nucleic acids.5
  • NPIDB: database of structures of nucleic acid - protein complexes.6
  • PDB_TF annotation: TF Annotation based on PDB IDs, (by GuoLab)
  • PDIdb: protein-DNA interface database.7
  • ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions.8
  • TF Modeller: building comparative TF-DNA complex models.9
  • WebPDA: comprehensive analysis of protein-DNA complex structures.10


1Bruno Contreras-Moreira. "3D-footprint: a database for the structural analysis of protein-DNA complexes." Nucleic Acids Res. 2010; 38(Database issue): D91-D97.
2Lee S, Blundell TL. "BIPA: a database for protein-nucleic acid interaction in 3D structures." Bioinformatics, 2009; 25(12):1559-60.
3Singh H. et al. "ccPDB: compilation and creation of data sets from Protein Data Bank." Nucleic Acids Res. 2012; 40(1): D486-9.
4Zhao, H. et al. Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function. Bioinformatics. 2010. 26(15), 1857.
5Berman HM. et al. "The Nucleic Acid Database: A Comprehensive Relational Database of Three-Dimensional Structures of Nucleic Acids." Biophys. J., 1992, 63, 751-759.
6Spirin S. et al. "NPIDB: a database of nucleic acids-protein interactions." Bioinformatics. 2007; 23(23): 3247-8.
7 Norambuena T. and Melo F. "The Protein-DNA Interface database." BMC Bioinformatics 2010, 11:262.
8Kumar MD. "ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions." Nucleic Acids Res. 2006; 34(Database issue): D204-6.
9Contreras-Moreira, B., Branger, P.A. & Collado-Vides, J. TFmodeller: comparative modelling of protein-DNA complexes. Bioinformatics. 2007. 23(13): 1694-1696.
10Kim, R. and Guo, J-T. "PDA: an automatic and comprehensive analysis program for protein-DNA complex structures." BMC Genomics, 10(Supple 1): S13, 2009.

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