d1cdwa1

Domain	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP family	Protein
1cdw_A1	d1cdwa1	A155-A242	Alpha and beta proteins (a+b)	TBP-like	TATA-box binding protein-like	TATA-box binding protein (TBP), C-terminal domain	TATA-box binding protein (TBP), C-terminal domain
1cdw_A2	d1cdwa2	A243-A333	Alpha and beta proteins (a+b)	TBP-like	TATA-box binding protein-like	TATA-box binding protein (TBP), C-terminal domain	TATA-box binding protein (TBP), C-terminal domain

Alignment-based scores

Aligner	Aligned Length	Sequence Identity	RMSD	GDT-TS	COMPASS
manual	88	0.27273	1.82016	82.10227	18.92926
dali	88	0.27273	1.81821	82.38636	19.03548
tm	87	0.27586	1.57086	83.90805	18.38185
fast	84	0.28571	1.40180	85.41667	20.61670

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