PASS2.8 - Home

solvent inaccessible: UPPER CASE X
solvent accesible: lower case x
alpha helix: red x

beta strand: blue x
3 - 10 helix: maroon x
hydrogen bond to main chain amide: bold x

hydrogen bond to mainchain carbonyl: underline x
disulphide bond: cedilla
positive phi: italic x

                             10        20        30        40        50  
d1ijqa1  ( 377 )    iAyLFFTNrheVrkMTld-----rseytslIpn-LrnVvALdTEVasnrI
d1npea-  ( 913 )    gthLLFAQtgkIerLpLerntMkkteAkaFlhipakvIIgLaFDçvdkvV
                      bbbbb    bbbbb           bbbb      bbbbbbb    bb

                             60        70        80        90        100 
d1ijqa1  ( 421 )    YWSDlsqrmIcstqly----dtVIsrdIqaPdgLAVDwihsnIYWTDsvl
d1npea-  ( 963 )    YWTDisepSIGrAsLhggepttiirqdLGsPegIaLdhlgrtIFWTDSql
                    bbbb    bbbbbb      bbbb        bbbbb    bbbbbb   

                             110       120       130       140       150 
d1ijqa1  ( 475 )    GTVSvAdtkGvkrktLfrengskPraIvVDPvhgfMYWTDwgt-pAkIkk
d1npea-  (1013 )    drIEvAkmdGtqrrvLfdtgLvnPrgIvTDpvrgnLYWTDwnrdnpkIET
                     bbbbbb      bbbb      bbbbbbb    bbbbbb      bbbb

                             160       170       180       190       200 
d1ijqa1  ( 524 )    GglnGvdiysLVtenIqwPngItLdLlsgrLYWVDSklhsISSIdvnggn
d1npea-  (1063 )    ShmdGtnrriLaqdnLglPNgLtFdafssqLÇWVDAgthrAEÇLnpaqpg
                    bb      bbbb      bbbbbbb    bbbbbb    bbbbbb     

                             210       220       230       240       250 
d1ijqa1  ( 574 )    rktIledekrLahPfSLAvfedkVFWTDiineAIfSAnrltGsdVnllAe
d1npea-  (1113 )    rrkvleg---LqyPFaVtsygkNLYYTDwktnSVIAmdlaiskemdtfhP
                     bbbbb       bbbbbbb  bbbbbb    bbbbbb       bbb  

                             260       270 
d1ijqa1  ( 624 )    n-LlsPedMvLfhnltqprg
d1npea-  (1160 )    hkqtrLygItIAlsqç    
                            bbbb

Domains
Outliers

Domain ID	Name	Family	Source	Domain	STRING-DB
d1ijqa1 # Domain Specific Files ATM file: Atomic coordinates by ASTRAL ATM2ALI file: Amino acid sequences by ATM2ALI SST file: Secondary structure by SSTRUC PSA file: solvent accessibility by PSA HBD file: Hydrogen bonds by HBOND PSE file: PyMol session file for conserved interactions PDBSUM1: Topological diagram d1ijqa1 # Links to other databases and tools RCSB-PDB: Research Collaboratory for Structural Bioinformatics SCOP: Structural Classification of Proteins EBI: European Bioinformatics Institute HOMSTRAD: Homologous Structure Alignment Database DDBASE: Dial-Derived Domain Database CATH: Class Architecture Topology and Homologous sfily PALI: Phylogeny and ALIgnment of homologous protein structures MODBASE: A Database of Annotated Comparative Protein Structure Models 3Dee: A Database of Protein Domain Definition PQS: Protein Quaternary Structure Query Form at the EBI LPC/CSU: Ligand-Protein Contacts & Contacts of Structural LPFC: A Library of Protein Family Cores MMDB: Molecular Modelling DataBase,NCBI CE: Databases and Tools for 3-D Protein Structure Comparison and Alignment PDBSUM: Summaries and structural analyses of PDB data files Pfam: Protein families database of alignments and HMMs	Low density lipoprotein (LDL) receptor	YWTD domain	Human (Homo sapiens) [TaxId: 9606]		view
d1npea- # Domain Specific Files ATM file: Atomic coordinates by ASTRAL ATM2ALI file: Amino acid sequences by ATM2ALI SST file: Secondary structure by SSTRUC PSA file: solvent accessibility by PSA HBD file: Hydrogen bonds by HBOND PSE file: PyMol session file for conserved interactions PDBSUM1: Topological diagram d1npea- # Links to other databases and tools RCSB-PDB: Research Collaboratory for Structural Bioinformatics SCOP: Structural Classification of Proteins EBI: European Bioinformatics Institute HOMSTRAD: Homologous Structure Alignment Database DDBASE: Dial-Derived Domain Database CATH: Class Architecture Topology and Homologous sfily PALI: Phylogeny and ALIgnment of homologous protein structures MODBASE: A Database of Annotated Comparative Protein Structure Models 3Dee: A Database of Protein Domain Definition PQS: Protein Quaternary Structure Query Form at the EBI LPC/CSU: Ligand-Protein Contacts & Contacts of Structural LPFC: A Library of Protein Family Cores MMDB: Molecular Modelling DataBase,NCBI CE: Databases and Tools for 3-D Protein Structure Comparison and Alignment PDBSUM: Summaries and structural analyses of PDB data files Pfam: Protein families database of alignments and HMMs	Nidogen	YWTD domain	Mouse (Mus musculus) [TaxId: 10090]		view

No outliers

Feature	Download
Superfamily
Distance Matrix
Conserved Interactions
Cusp Results
Alistat - Alignment Statistics
SMotif - Conserved Structural Motifs
MeanRMS
PCSSE Details
Absolutely Conserved Residues
Highly Conserved Residues

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I	A	Y	L	F	F	T	N	R	H	E	V	R	K	M	T	L	D	-	-	-	-	-	R	S	E	Y	T	S	L	I	P	N	-	L	R	N	V	V	A	L	D	T	E	V	A	S	N	R	I	Y	W	S	D	L	S	Q	R	M	I	C	S	T	Q	L	Y	-	-	-	-	D	T	V	I	S	R	D	I	Q	A	P	D	G	L	A	V	D	W	I	H	S	N	I	Y	W	T	D	S	V	L	G	T	V	S	V	A	D	T	K	G	V	K	R	K	T	L	F	R	E	N	G	S	K	P	R	A	I	V	V	D	P	V	H	G	F	M	Y	W	T	D	W	G	T	-	P	A	K	I	K	K	G	G	L	N	G	V	D	I	Y	S	L	V	T	E	N	I	Q	W	P	N	G	I	T	L	D	L	L	S	G	R	L	Y	W	V	D	S	K	L	H	S	I	S	S	I	D	V	N	G	G	N	R	K	T	I	L	E	D	E	K	R	L	A	H	P	F	S	L	A	V	F	E	D	K	V	F	W	T	D	I	I	N	E	A	I	F	S	A	N	R	L	T	G	S	D	V	N	L	L	A	E	N	-	L	L	S	P	E	D	M	V	L	F	H	N	L	T	Q	P	R	G
G	T	H	L	L	F	A	Q	T	G	K	I	E	R	L	P	L	E	R	N	T	M	K	K	T	E	A	K	A	F	L	H	I	P	A	K	V	I	I	G	L	A	F	D	C	V	D	K	V	V	Y	W	T	D	I	S	E	P	S	I	G	R	A	S	L	H	G	G	E	P	T	T	I	I	R	Q	D	L	G	S	P	E	G	I	A	L	D	H	L	G	R	T	I	F	W	T	D	S	Q	L	D	R	I	E	V	A	K	M	D	G	T	Q	R	R	V	L	F	D	T	G	L	V	N	P	R	G	I	V	T	D	P	V	R	G	N	L	Y	W	T	D	W	N	R	D	N	P	K	I	E	T	S	H	M	D	G	T	N	R	R	I	L	A	Q	D	N	L	G	L	P	N	G	L	T	F	D	A	F	S	S	Q	L	C	W	V	D	A	G	T	H	R	A	E	C	L	N	P	A	Q	P	G	R	R	K	V	L	E	G	-	-	-	L	Q	Y	P	F	A	V	T	S	Y	G	K	N	L	Y	Y	T	D	W	K	T	N	S	V	I	A	M	D	L	A	I	S	K	E	M	D	T	F	H	P	H	K	Q	T	R	L	Y	G	I	T	I	A	L	S	Q	C	-	-	-	-

Member	Chain	UniProtKB	GO term

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I	A	Y	L	F	F	T	N	R	H	E	V	R	K	M	T	L	D	-	-	-	-	-	R	S	E	Y	T	S	L	I	P	N	-	L	R	N	V	V	A	L	D	T	E	V	A	S	N	R	I	Y	W	S	D	L	S	Q	R	M	I	C	S	T	Q	L	Y	-	-	-	-	D	T	V	I	S	R	D	I	Q	A	P	D	G	L	A	V	D	W	I	H	S	N	I	Y	W	T	D	S	V	L	G	T	V	S	V	A	D	T	K	G	V	K	R	K	T	L	F	R	E	N	G	S	K	P	R	A	I	V	V	D	P	V	H	G	F	M	Y	W	T	D	W	G	T	-	P	A	K	I	K	K	G	G	L	N	G	V	D	I	Y	S	L	V	T	E	N	I	Q	W	P	N	G	I	T	L	D	L	L	S	G	R	L	Y	W	V	D	S	K	L	H	S	I	S	S	I	D	V	N	G	G	N	R	K	T	I	L	E	D	E	K	R	L	A	H	P	F	S	L	A	V	F	E	D	K	V	F	W	T	D	I	I	N	E	A	I	F	S	A	N	R	L	T	G	S	D	V	N	L	L	A	E	N	-	L	L	S	P	E	D	M	V	L	F	H	N	L	T	Q	P	R	G
G	T	H	L	L	F	A	Q	T	G	K	I	E	R	L	P	L	E	R	N	T	M	K	K	T	E	A	K	A	F	L	H	I	P	A	K	V	I	I	G	L	A	F	D	C	V	D	K	V	V	Y	W	T	D	I	S	E	P	S	I	G	R	A	S	L	H	G	G	E	P	T	T	I	I	R	Q	D	L	G	S	P	E	G	I	A	L	D	H	L	G	R	T	I	F	W	T	D	S	Q	L	D	R	I	E	V	A	K	M	D	G	T	Q	R	R	V	L	F	D	T	G	L	V	N	P	R	G	I	V	T	D	P	V	R	G	N	L	Y	W	T	D	W	N	R	D	N	P	K	I	E	T	S	H	M	D	G	T	N	R	R	I	L	A	Q	D	N	L	G	L	P	N	G	L	T	F	D	A	F	S	S	Q	L	C	W	V	D	A	G	T	H	R	A	E	C	L	N	P	A	Q	P	G	R	R	K	V	L	E	G	-	-	-	L	Q	Y	P	F	A	V	T	S	Y	G	K	N	L	Y	Y	T	D	W	K	T	N	S	V	I	A	M	D	L	A	I	S	K	E	M	D	T	F	H	P	H	K	Q	T	R	L	Y	G	I	T	I	A	L	S	Q	C	-	-	-	-

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I	A	Y	L	F	F	T	N	R	H	E	V	R	K	M	T	L	D	-	-	-	-	-	R	S	E	Y	T	S	L	I	P	N	-	L	R	N	V	V	A	L	D	T	E	V	A	S	N	R	I	Y	W	S	D	L	S	Q	R	M	I	C	S	T	Q	L	Y	-	-	-	-	D	T	V	I	S	R	D	I	Q	A	P	D	G	L	A	V	D	W	I	H	S	N	I	Y	W	T	D	S	V	L	G	T	V	S	V	A	D	T	K	G	V	K	R	K	T	L	F	R	E	N	G	S	K	P	R	A	I	V	V	D	P	V	H	G	F	M	Y	W	T	D	W	G	T	-	P	A	K	I	K	K	G	G	L	N	G	V	D	I	Y	S	L	V	T	E	N	I	Q	W	P	N	G	I	T	L	D	L	L	S	G	R	L	Y	W	V	D	S	K	L	H	S	I	S	S	I	D	V	N	G	G	N	R	K	T	I	L	E	D	E	K	R	L	A	H	P	F	S	L	A	V	F	E	D	K	V	F	W	T	D	I	I	N	E	A	I	F	S	A	N	R	L	T	G	S	D	V	N	L	L	A	E	N	-	L	L	S	P	E	D	M	V	L	F	H	N	L	T	Q	P	R	G
G	T	H	L	L	F	A	Q	T	G	K	I	E	R	L	P	L	E	R	N	T	M	K	K	T	E	A	K	A	F	L	H	I	P	A	K	V	I	I	G	L	A	F	D	C	V	D	K	V	V	Y	W	T	D	I	S	E	P	S	I	G	R	A	S	L	H	G	G	E	P	T	T	I	I	R	Q	D	L	G	S	P	E	G	I	A	L	D	H	L	G	R	T	I	F	W	T	D	S	Q	L	D	R	I	E	V	A	K	M	D	G	T	Q	R	R	V	L	F	D	T	G	L	V	N	P	R	G	I	V	T	D	P	V	R	G	N	L	Y	W	T	D	W	N	R	D	N	P	K	I	E	T	S	H	M	D	G	T	N	R	R	I	L	A	Q	D	N	L	G	L	P	N	G	L	T	F	D	A	F	S	S	Q	L	C	W	V	D	A	G	T	H	R	A	E	C	L	N	P	A	Q	P	G	R	R	K	V	L	E	G	-	-	-	L	Q	Y	P	F	A	V	T	S	Y	G	K	N	L	Y	Y	T	D	W	K	T	N	S	V	I	A	M	D	L	A	I	S	K	E	M	D	T	F	H	P	H	K	Q	T	R	L	Y	G	I	T	I	A	L	S	Q	C	-	-	-	-

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I	A	Y	L	F	F	T	N	R	H	E	V	R	K	M	T	L	D	-	-	-	-	-	R	S	E	Y	T	S	L	I	P	N	-	L	R	N	V	V	A	L	D	T	E	V	A	S	N	R	I	Y	W	S	D	L	S	Q	R	M	I	C	S	T	Q	L	Y	-	-	-	-	D	T	V	I	S	R	D	I	Q	A	P	D	G	L	A	V	D	W	I	H	S	N	I	Y	W	T	D	S	V	L	G	T	V	S	V	A	D	T	K	G	V	K	R	K	T	L	F	R	E	N	G	S	K	P	R	A	I	V	V	D	P	V	H	G	F	M	Y	W	T	D	W	G	T	-	P	A	K	I	K	K	G	G	L	N	G	V	D	I	Y	S	L	V	T	E	N	I	Q	W	P	N	G	I	T	L	D	L	L	S	G	R	L	Y	W	V	D	S	K	L	H	S	I	S	S	I	D	V	N	G	G	N	R	K	T	I	L	E	D	E	K	R	L	A	H	P	F	S	L	A	V	F	E	D	K	V	F	W	T	D	I	I	N	E	A	I	F	S	A	N	R	L	T	G	S	D	V	N	L	L	A	E	N	-	L	L	S	P	E	D	M	V	L	F	H	N	L	T	Q	P	R	G
G	T	H	L	L	F	A	Q	T	G	K	I	E	R	L	P	L	E	R	N	T	M	K	K	T	E	A	K	A	F	L	H	I	P	A	K	V	I	I	G	L	A	F	D	C	V	D	K	V	V	Y	W	T	D	I	S	E	P	S	I	G	R	A	S	L	H	G	G	E	P	T	T	I	I	R	Q	D	L	G	S	P	E	G	I	A	L	D	H	L	G	R	T	I	F	W	T	D	S	Q	L	D	R	I	E	V	A	K	M	D	G	T	Q	R	R	V	L	F	D	T	G	L	V	N	P	R	G	I	V	T	D	P	V	R	G	N	L	Y	W	T	D	W	N	R	D	N	P	K	I	E	T	S	H	M	D	G	T	N	R	R	I	L	A	Q	D	N	L	G	L	P	N	G	L	T	F	D	A	F	S	S	Q	L	C	W	V	D	A	G	T	H	R	A	E	C	L	N	P	A	Q	P	G	R	R	K	V	L	E	G	-	-	-	L	Q	Y	P	F	A	V	T	S	Y	G	K	N	L	Y	Y	T	D	W	K	T	N	S	V	I	A	M	D	L	A	I	S	K	E	M	D	T	F	H	P	H	K	Q	T	R	L	Y	G	I	T	I	A	L	S	Q	C	-	-	-	-