Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF SYG-2 D3-D4
 
Authors :  E. Ozkan, K. C. Garcia
Date :  15 Jan 14  (Deposition) - 19 Feb 14  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Immunoglobulin Superfamily, Cell Adhesion, Synaptogenesis, Protein Binding, N-Linked Glycosylation, Membrane, Extracellular, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Ozkan, P. H. Chia, R. R. Wang, N. Goriatcheva, D. Borek, Z. Otwinowski, T. Walz, K. Shen, K. C. Garcia
Extracellular Architecture Of The Syg-1/Syg-2 Adhesion Complex Instructs Synaptogenesis.
Cell(Cambridge, Mass. ) V. 156 482 2014
PubMed-ID: 24485456  |  Reference-DOI: 10.1016/J.CELL.2014.01.004

(-) Compounds

Molecule 1 - PROTEIN SYG-2
    Chains: A, B, C, D
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Strain: HIGH FIVE
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: D3-D4, UNP RESIDUES 231-430
    Gene: C26G2.1, CELE_C26G2.1, SYG-2
    Organism Common: NEMATODE
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:251 , THR A:253 , SER A:294BINDING SITE FOR MONO-SACCHARIDE NAG A 501 BOUND TO ASN A 251
2AC2SOFTWAREASP A:266 , ARG A:275 , ASN A:311 , NAG D:502BINDING SITE FOR MONO-SACCHARIDE NAG A 502 BOUND TO ASN A 311
3AC3SOFTWAREGLN A:351 , ASN A:391BINDING SITE FOR MONO-SACCHARIDE NAG A 503 BOUND TO ASN A 391
4AC4SOFTWAREPRO B:243 , ASN C:251 , SER C:294 , PHE C:295 , ILE C:296 , SER D:340 , ASN D:341 , LYS D:426BINDING SITE FOR MONO-SACCHARIDE NAG C 501 BOUND TO ASN C 251
5AC5SOFTWAREPRO A:243 , SER C:340 , ASN C:341 , ASN D:251 , SER D:294BINDING SITE FOR MONO-SACCHARIDE NAG D 501 BOUND TO ASN D 251
6AC6SOFTWARENAG A:502 , PHE D:337 , ASN D:349 , GLN D:351 , ASN D:391BINDING SITE FOR MONO-SACCHARIDE NAG D 502 BOUND TO ASN D 391

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:256 -A:308
2A:352 -A:410
3B:256 -B:308
4B:352 -B:410
5C:256 -C:308
6C:352 -C:410
7D:256 -D:308
8D:352 -D:410

(-) Cis Peptide Bonds  (11, 11)

Asymmetric Unit
No.Residues
1Asn A:242 -Pro A:243
2Asn A:262 -Pro A:263
3Asn A:358 -Pro A:359
4Asn B:242 -Pro B:243
5Asn B:262 -Pro B:263
6Asn B:358 -Pro B:359
7Asn C:242 -Pro C:243
8Asn C:262 -Pro C:263
9Asn C:358 -Pro C:359
10Asn D:262 -Pro D:263
11Asn D:358 -Pro D:359

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OFP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OFP)

(-) Exons   (0, 0)

(no "Exon" information available for 4OFP)

(-) Sequences/Alignments

Asymmetric 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:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....ee...eeeeeeeee......eeeeee..ee.....ee.....eeeeeeeee.........eeeeee....eee.....ee.....eeee...eee...eeeeeeee.........eeee..ee......eeeee..eeeeeeeeeee.........eeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ofp A 230 DPPSDPTVEILRNPSALRSGDNVTIACSVTGGNPPPDVFWYHENKRLQSHSTLDTRSKEIKNIYSFIASQNDNMAEYECRANNSRPKRKAMKLEVNYPPASVELFGESNIRYGSSANIQCKSLPSNPASQITWIINGRSVPTPTQREFVVENGIVSSSNVSVHSNELSVEAHQINVECMATNPEGSSAKQHVIKIIA 429
                                   239       249       259       269       279       289       299       309    || 322       332       342       352       362       372       382       392       402       412       422       
                                                                                                              314|                                                                                                               
                                                                                                               318                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....ee...eeeeeeee.......eeeeee..ee.....ee......eeeeeeee........eeeeeee....eeeeee..ee.....eeee...eee...eeeeeeee.......eeeeee..ee......eeeee..eeeeeeeeeee.........eeeeeeeee....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ofp B 234 DPTVEILRNPSALRSGDNVTIACSVTGGNPPPDVFWYHENKRLQSHSTLDTRSKEIKNIYSFIASQNDNMAEYECRANNSRPKRKAMKLEVNYPPASVELFGESNIRYGSSANIQCKSLPSNPASQITWIINGRSVPTPTQREFVVENGIVSSSNVSVHSNELSVEAHQINVECMATNPEGSSAKQHVIKIIAP 430
                                   243       253       263       273       283       293       303       313||     326       336       346       356       366       376       386       396       406       416       426    
                                                                                                          314|                                                                                                                
                                                                                                           318                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:193
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....ee...eeeeeeee........eeeee.........ee......eeeeeeee.........eeeee......ee.....ee.....eeee...eee...eeeeeeee.......eeeeee..eee.....eeeee..eeeeeeeeeee.........eeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ofp C 234 DPTVEILRNPSALRSGDNVTIACSVTGGNPPPDVFWYHENKRLQSHSTLDTRSKEIKNIYSFIASQNDNMAEYECRANNSRPKRKAMKLEVNYPPASVELFGESNIRYGSSANIQCKSLPSNPASQITWIINGRSVPTPTQREFVVENGIVSSSNVSVHSNELSVEAHQINVECMATNPEGSSAKQHVIKIIA 429
                                   243       253       263       273       283       293       303       313||     326       336       346       356       366       376       386       396       406       416       426   
                                                                                                          314|                                                                                                               
                                                                                                           318                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.....ee...eeeeeeeee......eeeeee.........ee.....eeeeeeeee.........eeeeee.....ee.....ee.....eeee...eee...eeeeeeee.......eeeeee..eee.....eeeee..eeeeeeeeeee.........eeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ofp D 230 DPPSDPTVEILRNPSALRSGDNVTIACSVTGGNPPPDVFWYHENKRLQSHSTLDTRSKEIKNIYSFIASQNDNMAEYECRANNSRPKRKAMKLEVNYPPASVELFGESNIRYGSSANIQCKSLPSNPASQITWIINGRSVPTPTQREFVVENGIVSSSNVSVHSNELSVEAHQINVECMATNPEGSSAKQHVIKIIA 429
                                   239       249       259       269       279       289       299       309    || 322       332       342       352       362       372       382       392       402       412       422       
                                                                                                              314|                                                                                                               
                                                                                                               318
   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 4OFP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OFP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OFP)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    NAG  [ 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 ]
 
  Cis Peptide Bonds
    Asn A:242 - Pro A:243   [ RasMol ]  
    Asn A:262 - Pro A:263   [ RasMol ]  
    Asn A:358 - Pro A:359   [ RasMol ]  
    Asn B:242 - Pro B:243   [ RasMol ]  
    Asn B:262 - Pro B:263   [ RasMol ]  
    Asn B:358 - Pro B:359   [ RasMol ]  
    Asn C:242 - Pro C:243   [ RasMol ]  
    Asn C:262 - Pro C:263   [ RasMol ]  
    Asn C:358 - Pro C:359   [ RasMol ]  
    Asn D:262 - Pro D:263   [ RasMol ]  
    Asn D:358 - Pro D:359   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 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
  4ofp
    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
  SYG2_CAEEL | Q9U3P2
    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
  SYG2_CAEEL | Q9U3P2
    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
        SYG2_CAEEL | Q9U3P2: 4ofk 4ofy

(-) Related Entries Specified in the PDB File

4of0 4of3 4of6 4of7 4of8 4ofd 4ofi 4ofk 4ofy