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 SOX9
Homo sapiens
 HIF1A
Homo sapiens
 Pax6
Mus musculus
 PAX6
Homo sapiens
 Snai2
Mus musculus
 PPARA
Homo sapiens
 Ppara
Mus musculus
 Thrb
Mus musculus
 SNAI2
Homo sapiens
 Tbr1
Mus musculus
Transcription Factor Encyclopedia  BETA
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Overview
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Structures
About this section
This section contains 3D PDB models of structural predictions for this transcription factor. METHODS: The template selection protocol follows that of Morozov and Siggia, in which templates are selected to optimize similarity of DNA-binding residues (Morozov AV, Siggia ED. PNAS 104(17):7068-73). This has been shown to increase modeling accuracy at the DNA-binding interface. For all solved structures containing DNA, amino acids within 4A of DNA (DNA-binding residues) are stored. Pfam domain hits of each DNA-bound chain are detected by hmmer, and each hit is added to a list mapping domain family name to chain hits. Pfam domain hits of each unsolved structure are detected by HMMER. For each identified Pfam family, the unsolved sequence is aligned to all solved family members (putative templates). Alignments are scored based on similarity of the DNA-binding residues in the template to the aligned residues of the unsolved sequence. For each subsequence of the unsolved protein identified as a DNA-binding domain, the top scoring template is selected. For sequences known to form homodimers, a homodimeric template is selected. The model is constructed from the template using Modeller 9v2. DNA bound to the template is added to the model by superimposition of the solved and modeled structures.
Arntl 11865 HLH 1nkpD
Image 3D Model .PDB File
Family
Zipper-Type Group » Helix-Loop-Helix Family
AHR
Homo sapiens
Ahr
Mus musculus
 ARNT
Homo sapiens
 Arnt
Mus musculus
Arnt2
Mus musculus
 ARNTL
Homo sapiens
 Arntl
Mus musculus
Ascl1
Mus musculus
Ascl3
Mus musculus
Atoh1
Mus musculus
Atoh8
Mus musculus
Bhlhb2
Mus musculus
Bhlhb3
Mus musculus
 CLOCK
Homo sapiens
 Clock
Mus musculus
Ebf1
Mus musculus
 EPAS1
Homo sapiens
 Epas1
Mus musculus
Figla
Mus musculus
Hand1
Mus musculus
Hand2
Mus musculus
Helt
Mus musculus
Hes2
Mus musculus
Hes3
Mus musculus
Hes5
Mus musculus
 Hif1a
Mus musculus
 HIF1A
Homo sapiens
Max
Mus musculus
Mesp2
Mus musculus
Mitf
Mus musculus
Mlx
Mus musculus
Mlxipl
Mus musculus
Mnt
Mus musculus
Msc
Mus musculus
Mxd1
Mus musculus
Mxi1
Mus musculus
Myc
Mus musculus
Mycn
Mus musculus
Myf5
Mus musculus
Myf6
Mus musculus
Myod1
Mus musculus
Myog
Mus musculus
Neurod1
Mus musculus
Neurod2
Mus musculus
Neurod6
Mus musculus
Neurog1
Mus musculus
Neurog3
Mus musculus
Nhlh1
Mus musculus
Nhlh2
Mus musculus
Npas1
Mus musculus
Npas2
Mus musculus
Npas3
Mus musculus
Npas4
Mus musculus
Olig1
Mus musculus
Olig2
Mus musculus
Olig3
Mus musculus
 PTF1A
Homo sapiens
 Ptf1a
Mus musculus
Scx
Mus musculus
Sim2
Mus musculus
Srebf1
Mus musculus
Srebf2
Mus musculus
Tal1
Mus musculus
Tal2
Mus musculus
Tcf12
Mus musculus
Tcf15
Mus musculus
Tcf4
Mus musculus
Tcfap2a
Mus musculus
Tcfap2b
Mus musculus
Tcfap2e
Mus musculus
Tcfap4
Mus musculus
 Tcfe2a
Mus musculus
Tcfe3
Mus musculus
Tcfec
Mus musculus
 Twist1
Mus musculus
 TWIST1
Homo sapiens
Twist2
Mus musculus
Usf1
Mus musculus
Usf2
Mus musculus
 
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