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  
d1bb8a-  (   3 )                           ekrrDnrgrilktgesqrk----dgrY
d1gcca-  ( 144 )                                    khyrgvrqrp----wgkf
d1ub1a-  (  72 )    apavpeasaspkqrrsiirdrgpmyddptlpegwtrklkqrksgrsagky
d1z1ba1  (  11 )                                    dlppnLyirn----ngyy
d2ky8a-  (   3 )                       dkqgrtdCpAlppgwkkeevirksglsagks
d3vxva-  (  72 )                                pvpcgwervvkqrlsgktagkf
                                                         bbb         b

                             60        70        80        90        100 
d1bb8a-  (  26 )    lykYidsf---gepqfvySwklvatdrvpagkrdciSlrekiaelqkdih
d1gcca-  ( 158 )    AAeirDpakngarvwlgtfetaedAAl---------aYdraAfrmrgsrA
d1ub1a-  ( 122 )    dvylinpqg-----kaFrskveliayfekvgdtsldpndfdFtvtgrgsp
d1z1ba1  (  25 )    cyr--dpr---tgkefglgrdrriAit---------eAiqanielfsg--
d2ky8a-  (  34 )    dvyYfSpsg-----kkFrskpqlarylgnavdls-----cFdfrtGkmm 
d3vxva-  (  94 )    dvyfiSpqg-----lkfrskrslanyll---------------kngetfl
                    bbbbb          bb    aaaaaa                       

                             110       120       130 
d1bb8a-  (  73 )    d                                
d1gcca-  ( 199 )    llnfpl-------------------------rv
d1ub1a-  ( 167 )    s---rreqrppkkakspkspgsgrgrgrpkgsg
d1z1ba1  (  59 )    h                                
d2ky8a-                                              
d3vxva-  ( 124 )    kpedfnftvlpk

Domains
Outliers

Domain ID	Name	Family	Source	STRING-DB
d1bb8a- # 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 d1bb8a- # 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	DNA-binding domain from tn916 integrase	DNA-binding domain from tn916 integrase	Enterococcus faecalis [TaxId: 1351]	view
d1gcca- # 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 d1gcca- # 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	GCC-box binding domain	GCC-box binding domain	Thale cress (Arabidopsis thaliana) [TaxId: 3702]	view
d1ub1a- # 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 d1ub1a- # 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	Methyl-CpG-binding protein 2, MECP2	Methyl-CpG-binding domain, MBD	Chicken (Gallus gallus) [TaxId: 9031]	view
d1z1ba1 # 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 d1z1ba1 # 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	lambda integrase N-terminal domain	lambda integrase N-terminal domain	Bacteriophage lambda [TaxId: 10710]	view
d2ky8a- # 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 d2ky8a- # 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	automated matches	automated matches	Chicken (Gallus gallus) [TaxId: 9031]	view
d3vxva- # 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 d3vxva- # 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	automated matches	automated matches	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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Member	Chain	UniProtKB	GO term
d1bb8a_	A	P22886	GO:0003677
d1bb8a_	A	P22886	GO:0008907
d1bb8a_	A	P22886	GO:0015074
d1gcca_	A	O80337	GO:0003677
d1gcca_	A	O80337	GO:0003700
d1gcca_	A	O80337	GO:0006355
d1gcca_	A	O80337	GO:0009873
d1ub1a_	A	O42403	GO:0003677
d1z1ba1	A	P03700	GO:0003677
d1z1ba1	A	P03700	GO:0006310
d1z1ba1	A	P03700	GO:0008907
d1z1ba1	A	P03700	GO:0015074
d1z1ba1	A	P03700	GO:0016740
d1z1ba1	A	P03700	GO:0016787
d1z1ba1	A	P03700	GO:0032359
d1z1ba1	A	P03700	GO:0044826
d1z1ba1	A	P03700	GO:0046718
d1z1ba1	A	P03700	GO:0075713

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

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