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 :  STRUCTURE OF RABPHILIN C2A DOMAIN BOUND TO IP3
 
Authors :  J. Guillen, C. Ferrer-Orta, M. Buxaderas, D. Perez-Sanchez, M. Guerre Valero, G. Luengo-Gil, J. Pous, P. Guerra, J. C. Gomez-Fernandez, N. V S. Corbalan-Garcia
Date :  21 Nov 13  (Deposition) - 25 Dec 13  (Release) - 25 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym./Biol. Unit :  A
Keywords :  Rabphilin-3A, C2 Domain, C2A, Calcium Binding, Synaptic Exocytosis Metal-Binding, Protein Transport, C-2 Domain Fold, Exophilin-1 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Guillen, C. Ferrer-Orta, M. Buxaderas, D. Perez-Sanchez, M. Guerrero-Valero, G. Luengo-Gil, J. Pous, P. Guerra, J. C. Gomez-Fernandez, N. Verdaguer, S. Corbalan-Garcia
Structural Insights Into The Ca2+ And Pi(4, 5)P2 Binding Modes Of The C2 Domains Of Rabphilin 3A And Synaptotagmin 1
Proc. Natl. Acad. Sci. Usa 2013
PubMed-ID: 24302762  |  Reference-DOI: 10.1073/PNAS.1316179110

(-) Compounds

Molecule 1 - RABPHILIN-3A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C2 DOMAIN, UNP RESIDUES 378-510
    Gene: RPH3A
    Organism Common: BROWN RAT,RAT,RATS
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: EXOPHILIN-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1I3P1Ligand/IonD-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:410 , PRO A:411 , MET A:412 , TYR A:421 , LYS A:423 , HIS A:425 , LYS A:435 , ARG A:437 , ASN A:481 , SO4 A:602 , HOH A:702 , HOH A:763 , HOH A:764 , HOH A:803BINDING SITE FOR RESIDUE I3P A 601
2AC2SOFTWARELYS A:423 , ARG A:442 , ARG A:469 , SER A:471 , PHE A:483 , I3P A:601BINDING SITE FOR RESIDUE SO4 A 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NP9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:427 -Pro A:428

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NP9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NP9)

(-) Exons   (0, 0)

(no "Exon" information available for 4NP9)

(-) 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:129
                                                                                                                                                                 
               SCOP domains d4np9a_ A: automated matches                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeehhh.eeeeeeeeee............eeeeeeee...hhh.eee..........eeeeeeeee..hhhhhhhheeeeeeeee.....eeeeeeeeee.hhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4np9 A 382 TLGALEFSLLYDQDNSNLQCTIIRAKGLKPMDSNGLADPYVKLHLLPGASKSNKLRTKTLRNTRNPVWNETLQYHGITEEDMQRKTLRISVCDEDKFGHNEFIGETRFSLKKLKANQRKNFNICLERVI 510
                                   391       401       411       421       431       441       451       461       471       481       491       501
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NP9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NP9)

(-) Gene Ontology  (34, 34)

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
    I3P  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:427 - Pro A:428   [ 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
  4np9
    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
  RP3A_RAT | P47709
    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
  RP3A_RAT | P47709
    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
        RP3A_RAT | P47709: 1zbd 2chd 2cm5 2cm6 3rpb 4lt7 4ns0 5lo8 5lob 5low

(-) Related Entries Specified in the PDB File

2chd CRYSTAL STRUCTURE OF THE C2A DOMAIN OF RABPHILIN-3A
2cm5 CRYSTAL STRUCTURE OF THE C2B DOMAIN OF RABPHILIN
2cm6 CRYSTAL STRUCTURE OF THE C2B DOMAIN OF RABPHILIN 3A
2k3h STRUCTURAL DETERMINANTS FOR CA2+ AND PIP2 BINDING BY THE C2A DOMAIN OF RABPHILIN-3A
4ns0