d1cdwa1

DomainSCOPidRangeSCOP ClassSCOP FoldSCOP SuperfamilySCOP familyProtein
1cdw_A1d1cdwa1A155-A242Alpha and beta proteins (a+b)TBP-likeTATA-box binding protein-likeTATA-box binding protein (TBP), C-terminal domainTATA-box binding protein (TBP), C-terminal domain
1cdw_A2d1cdwa2A243-A333Alpha and beta proteins (a+b)TBP-likeTATA-box binding protein-likeTATA-box binding protein (TBP), C-terminal domainTATA-box binding protein (TBP), C-terminal domain

Alignment-based scores

AlignerAligned LengthSequence IdentityRMSDGDT-TSCOMPASS
manual880.272731.8201682.1022718.92926
dali880.272731.8182182.3863619.03548
tm870.275861.5708683.9080518.38185
fast840.285711.4018085.4166720.61670

In the alignments below, two upper-case letters are aligned, and two lower-case letters are NOT aligned. The superposition files are re-constructed from the corresponding alignments by minimizing the overall RMSD. In a PDB-format superposition file, the first domain is represented by chain S and the second domain is represented by chain A. The coordinates of the first domain are transformed, while the coordinates of the second domain are the same as in the original PDB file.


MANUAL alignment      superposition in PDB format     colored superposition in PyMol

1cdw_A1   --SGIVPQLQNIVSTVNLGCKLDLKTIALRAR-NAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEENSRLAARKYARVVQKLGF
1cdw_A2   paKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQqFSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK

DALI alignment      superposition in PDB format     colored superposition in PyMol

1cdw_A1   --SGIVPQLQNIVSTVNLGCKLDLKTIALRA-RNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEENSRLAARKYARVVQKLGF
1cdw_A2   paKFLDFKIQNMVGSCDVKFPIRLEGLVLTHqQFSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK

TM alignment      superposition in PDB format     colored superposition in PyMol

1cdw_A1   --SGIVPQLQNIVSTVNLGCKLDLKTIALRA-RNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEENSRLAARKYARVVQKLGF-
1cdw_A2   PAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQFSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILK-GFRK

FAST alignment      superposition in PDB format     colored superposition in PyMol

1cdw_A1   SG----IVPQLQNIVSTVNLGCKLDLKTIALRA-RNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEENSRLAARKYARVVQKLGF--
1cdw_A2   --PAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQFSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGF--RK