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 :  CRYSTAL STRUCTURE OF RABEX-5CC AND RABAPTIN-5C21 COMPLEX
 
Authors :  Z. Zhang, T. Zhang, J. Ding
Date :  08 Oct 13  (Deposition) - 23 Jul 14  (Release) - 09 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Rab5, Rabex-5, Rabaptin-5, Gef Activity, Endocytosis, Early Endosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, T. Zhang, S. Wang, Z. Gong, C. Tang, J. Chen, J. Ding
Molecular Mechanism For Rabex-5 Gef Activation By Rabaptin-
Elife V. 3 02687 2014
PubMed-ID: 24957337  |  Reference-DOI: 10.7554/ELIFE.02687

(-) Compounds

Molecule 1 - RAB5 GDP/GTP EXCHANGE FACTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET1
    Expression System Strain: BL21(DE3) CODON PLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 630-672
    Gene: RABEX5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RAP1, RABAPTIN-5-ASSOCIATED EXCHANGE FACTOR FOR RAB5, RABEX- 5
 
Molecule 2 - RAB GTPASE-BINDING EFFECTOR PROTEIN 1
    Chains: B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET1
    Expression System Strain: BL21(DE3) CODON PLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 552-642
    Gene: RABEP1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RABAPTIN-4, RABAPTIN-5, RABAPTIN-5ALPHA, RENAL CARCINOMA ANTIGEN NY-REN-17

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4N3Y)

(-) Sites  (0, 0)

(no "Site" information available for 4N3Y)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N3Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4N3Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N3Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N3Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4N3Y)

(-) 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:35
                                                                   
               SCOP domains ----------------------------------- SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                 4n3y A 419 QLNERQERIMNEAKKLEKDLIDWTDGIAREVQDIV 453
                                   428       438       448     


Chain B from PDB  Type:PROTEIN  Length:83
                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 4n3y B 552 ETRDQVKKLQLMLRQANDQLEKTMKDKQELEDFIKQSSEDSSHQISALVLRAQASEILLEELQQGLSQAKRDVQEQMAVLMQS 634
                                   561       571       581       591       601       611       621       631   


Chain C from PDB  Type:PROTEIN  Length:83
                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 4n3y C 552 ETRDQVKKLQLMLRQANDQLEKTMKDKQELEDFIKQSSEDSSHQISALVLRAQASEILLEELQQGLSQAKRDVQEQMAVLMQS 634
                                   561       571       581       591       601       611       621       631
   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 4N3Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N3Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N3Y)

(-) Gene Ontology  (37, 46)

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 4n3y)
 
  Sites
(no "Sites" information available for 4n3y)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4n3y)
 

(-) 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
  4n3y
    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
  RABE1_HUMAN | Q15276
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  RABX5_HUMAN | Q9UJ41
    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
  RABE1_HUMAN | Q15276
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  RABX5_HUMAN | Q9UJ41
    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
        RABE1_HUMAN | Q15276: 1p4u 1tu3 1x79 4n3z 4q9u
        RABX5_HUMAN | Q9UJ41: 1txu 2c7m 2c7n 2ot3 4n3x 4n3z 4q9u

(-) Related Entries Specified in the PDB File

4n3x 4n3z