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

(-) Description

Title :  SYNAPTONEMAL COMPLEX PROTEIN
 
Authors :  J. Feng, S. Fu, X. Cao, H. Wu, J. Lu, M. Zeng, L. Liu, X. Yang, Y. Shen
Date :  23 Mar 16  (Deposition) - 29 Mar 17  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Component Of Synaptonemal Complexes, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Feng, S. Fu, X. Cao, H. Wu, J. Lu, M. Zeng, L. Liu, X. Yang, Y. Shen
Structure Of Synaptonemal Complexes Protein At 2. 6 Anstroms Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SYNAPTONEMAL COMPLEX PROTEIN 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-390
    Gene: SYCP2, SCP2
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: SCP-2,SYNAPTONEMAL COMPLEX LATERAL ELEMENT PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5IWZ)

(-) Sites  (0, 0)

(no "Site" information available for 5IWZ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IWZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5IWZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IWZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IWZ)

(-) Exons   (0, 0)

(no "Exon" information available for 5IWZ)

(-) 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:372
                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh.hhhhhhhh.........eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..eehhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee..eeee..ee............eeeee....eeee....eeee...eeeeeeeee..eeeeeeeeeeeeee..eeeeeeeeeee...hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5iwz A   1 MPVRPDLQQLEKCIDDALRKNDFKPLLALLQIDICEDVKIKCSKQFLRKLDDLICRELNKKDIQTVSSILISIGRCSKNIFILGQAGLQTMIKQGLVQKMVSWFENSKEIILNQDEAVMNMIEDLFDLLMVIYDISDEGKNQVLESFIPQICALVIDSRVNFCIQQEALKKMNLMLDRINQEMLTLMSNMGERILDVGDYELQVGIVEALCRMTTEKRRQELAYEWFSMDFIANAFKEIKDCEFETDCRIFLNLVNGILGDKRRVYTFPCLSAFLGKYELQIPSDEKLEEFWIDFNLGSHTLSFYIEAVTVPEEKVQMYNIEVRESKKLLTLTLKNIVKISKKEGKELLFYFDESLEITNVTKKVFGGLEHH 394
                                    10        20        30        40        50        60        70        80        90       100       110   ||  124       134       144       154       164       174       193       203       213       223       233       243       253       263       273       283       293       303       313     ||332       342       352       362       372       382       392  
                                                                                                                                           114|                                                             183|                                                                                                                           319|                                                                 
                                                                                                                                            119                                                              193                                                                                                                            329
   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 5IWZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IWZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IWZ)

(-) Gene Ontology  (17, 17)

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
(no "Ligands, Modified Residues, Ions" information available for 5iwz)
 
  Sites
(no "Sites" information available for 5iwz)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5iwz)
 

(-) 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 ](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
  5iwz
    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
  SYCP2_MOUSE | Q9CUU3
    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
  SYCP2_MOUSE | Q9CUU3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 5IWZ)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5IWZ)