Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  SORLA VPS10P DOMAIN IN LIGAND-FREE FORM
 
Authors :  Y. Kitago, Z. Nakata, M. Nagae, T. Nogi, J. Takagi
Date :  30 Mar 14  (Deposition) - 04 Feb 15  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Propeller, Receptor, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kitago, M. Nagae, Z. Nakata, M. Yagi-Utsumi, S. Takagi-Niidome, E. Mihara, T. Nogi, K. Kato, J. Takagi
Structural Basis For Amyloidogenic Peptide Recognition By Sorla
Nat. Struct. Mol. Biol. 2015
PubMed: search  |  Reference-DOI: 10.1038/NSMB.2954

(-) Compounds

Molecule 1 - SORTILIN-RELATED RECEPTOR
    Chains: A
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHO CELLS
    Expression System Common: CHINESE HAMSTER
    Expression System Plasmid: PEF
    Expression System Taxid: 10029
    Expression System Variant: LEC 3.2.8.1
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN, UNP RESIDUES 29-753
    Gene: SORL1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NEURONAL EXTRACELLULAR RECEPTOR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:249 , HIS A:269 , GLU A:270 , GLY A:273 , ARG A:298 , SER A:399BINDING SITE FOR RESIDUE PO4 A 804
02AC2SOFTWAREARG A:303 , ASP A:353 , ARG A:416 , EDO A:812 , HOH A:978 , HOH A:1021BINDING SITE FOR RESIDUE PO4 A 805
03AC3SOFTWAREVAL A:106 , HIS A:108 , ARG A:122 , GLN A:166 , PHE A:167BINDING SITE FOR RESIDUE PO4 A 806
04AC4SOFTWAREASP A:173 , ARG A:176 , SER A:216 , HOH A:997BINDING SITE FOR RESIDUE PO4 A 807
05AC5SOFTWAREGLU A:348 , TYR A:349 , TYR A:350 , CYS A:362 , SER A:364 , HIS A:365 , HOH A:938BINDING SITE FOR RESIDUE EDO A 808
06AC6SOFTWARESER A:524 , LYS A:631 , ARG A:653BINDING SITE FOR RESIDUE EDO A 809
07AC7SOFTWAREGLU A:348 , ASP A:400 , ARG A:404BINDING SITE FOR RESIDUE EDO A 810
08AC8SOFTWARELYS A:381 , ASP A:685 , ARG A:729BINDING SITE FOR RESIDUE EDO A 811
09AC9SOFTWAREALA A:352 , PHE A:414 , ARG A:416 , PO4 A:805BINDING SITE FOR RESIDUE EDO A 812
10BC1SOFTWAREPHE A:191 , CYS A:699 , ARG A:726 , TYR A:728 , HOH A:913 , HOH A:997 , HOH A:1035BINDING SITE FOR RESIDUE EDO A 813
11BC2SOFTWAREPHE A:154 , ASN A:158 , SER A:160 , ALA A:184BINDING SITE FOR MONO-SACCHARIDE NAG A 801 BOUND TO ASN A 158
12BC3SOFTWARETYR A:93 , ASN A:616 , THR A:618BINDING SITE FOR MONO-SACCHARIDE NAG A 802 BOUND TO ASN A 616
13BC4SOFTWAREVAL A:672 , ASN A:674 , THR A:735BINDING SITE FOR MONO-SACCHARIDE NAG A 803 BOUND TO ASN A 674

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:625 -A:660
2A:643 -A:675
3A:677 -A:736
4A:684 -A:699

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:256 -Pro A:257

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WSX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WSX)

(-) Exons   (0, 0)

(no "Exon" information available for 3WSX)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:606
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee.....eeeeee.......eeeeee.....eeeeee.......ee.hhhh...........eeeeee.......eeeee....eeeee.......eeee......eeee.......eeeee......eeeee.......eeee..eeeeee..........eeeee......eeeeee.....hhh.eeeeeeee..eeee..eeeeeeee....eeeeeeee.....ee............eeee......eeee.hhh.eeeeee........eeeeeeee.......................eee.......eeeee...eeeee.......ee.ee..eeeeeee.eee........eeeeeee....eeeee.......eeeee..eeeeeehhhheeeeee......eeeee.......eeee......eeeeeee.......eeeeeee...eeeeeee.hhhhh...hhh.eeee.........hhh.eeeeeeee................eeee...hhh.eee...eee..hhhhh.eee.hhhh..........eee...eee.................eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3wsx A  89 PIKVYGQVSLNDSHNQMVVHWAGEKSNVIVALARDSPKSSDVYVSYDYGKSFKKISDKLNFGLGNRSEAVIAQFYHSPADNKRYIFADAYAQYLWITFDFCNTLQGFSIPFRAADLLLHSKASNLLLGFDRSHPNKQLWKSDDFGQTWIMIQEHVKSFSWGIDPYDKPNTIYIERHEPSGYSTVFRSTDFFQSRENQEVILEEVRDFQLRDKYMFATKVVHQQSSVQLWVSFGRKPMRAAQFVTRHPINEYYIADASEDQVFVCVSHSNNRTNLYISEAEGLKFSLSLENVLYYSPGGAGSDTLVRYFANEPFADFHRVEGLQGVYIATLINMRSVITFDKGGTWEFLQAPGCSLHLAQMPILSKESAPGLIIATGSVGKKTNVYISSSAGARWREALPGPHYYTWGDHGGIITAIAQGMETNELKYSTNEGETWKTFIFSEKPVFVYGLLTEPGEKSTVFTIFGSNHSWLILQVNATDALGVPCTENDYKLWSPSDERGNECLLGHKTVFKRRTPHATCFNGEDFDRPVVVSNCSCTREDYECDFGFKMSEDLSLEVCVPDPEFSGKSYSPVGSTYRRTRGYRKISGDTCSGGDVEARLEGELVP 751
                                    98       108       118     ||133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313||     328       338       348       358       368       378       388       398       408       418       428||     445       455||     492       502       512|      526       536       546       556       566       576       586       596      |610       620       630       640       650       660       670       680       690       700       710 ||    725       735       745      
                                                             124|                                                                                                                                                                                     314|                                                                                                          429|                456|    479|                 512|                                                                                   603|                                                                                                     712|                                 
                                                              130                                                                                                                                                                                      320                                                                                                           437                 472     492                  517                                                                                    608                                                                                                      718
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3WSX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WSX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WSX)

(-) Gene Ontology  (52, 52)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:256 - Pro A:257   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3wsx
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SORL_HUMAN | Q92673
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SORL_HUMAN | Q92673
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SORL_HUMAN | Q92673: 2dm4 3g2s 3g2t 3wsy 3wsz

(-) Related Entries Specified in the PDB File

3wsy SAME PROTEIN COMPLEX WITH ITS OWN PROPEPTIDE FRAGMENT
3wsz SAME PROTEIN COMPLEX WITH ABETA-DERIVED PEPTIDE