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
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)

(-) Description

Title :  DROSOPHILA MELANOGASTER RAB3 BOUND TO GMPPNP
 
Authors :  J. A. Lardong, J. H. Driller, H. Depner, C. Weise, A. Petzoldt, M. C. Wahl S. J. Sigrist, B. Loll
Date :  13 Oct 14  (Deposition) - 10 Dec 14  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Gtp Hydrolysis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Lardong, J. H. Driller, H. Depner, C. Weise, A. Petzoldt, M. C. Wahl, S. J. Sigrist, B. Loll
Structures Of Drosophila Melanogaster Rab2 And Rab3 Bound T Gmppnp.
Acta Crystallogr F Struct V. 71 34 2015 Biol Commun
PubMed-ID: 25615965  |  Reference-DOI: 10.1107/S2053230X1402617X

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN RAB-3
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-MBP
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: GTPASE DOMAIN (UNP RESIDUES 1-188)
    Gene: RAB3, CG7576
    Mutation: YES
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
11PE4Ligand/IonPENTAETHYLENE GLYCOL
2GNP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:30 , SER A:31 , VAL A:32 , GLY A:33 , LYS A:34 , THR A:35 , SER A:36 , PHE A:46 , THR A:47 , SER A:48 , ALA A:49 , PHE A:50 , SER A:52 , THR A:53 , GLY A:79 , ASN A:134 , LYS A:135 , ASP A:137 , MET A:138 , SER A:164 , ALA A:165 , LYS A:166 , MG A:202 , HOH A:301 , HOH A:302 , HOH A:307 , HOH A:310 , HOH A:380 , HOH A:422 , HOH A:423BINDING SITE FOR RESIDUE GNP A 201
2AC2SOFTWARETHR A:35 , THR A:53 , GNP A:201 , HOH A:301 , HOH A:302BINDING SITE FOR RESIDUE MG A 202
3AC3SOFTWAREPHE A:50 , SER A:52 , VAL A:54 , ARG A:82 , HOH A:330 , HOH A:403 , SER B:45 , HOH B:381BINDING SITE FOR RESIDUE 1PE A 203
4AC4SOFTWAREGLU A:81 , ARG A:84 , ASP A:114 , TRP A:115 , GLN A:118 , HOH A:489BINDING SITE FOR RESIDUE 1PE A 204
5AC5SOFTWARESER B:30 , SER B:31 , VAL B:32 , GLY B:33 , LYS B:34 , THR B:35 , SER B:36 , PHE B:46 , THR B:47 , SER B:48 , PHE B:50 , SER B:52 , THR B:53 , GLY B:79 , ASN B:134 , LYS B:135 , ASP B:137 , MET B:138 , SER B:164 , ALA B:165 , LYS B:166 , MG B:202 , HOH B:302 , HOH B:307 , HOH B:317 , HOH B:331 , HOH B:352 , HOH B:417 , HOH B:450BINDING SITE FOR RESIDUE GNP B 201
6AC6SOFTWARETHR B:35 , THR B:53 , GNP B:201 , HOH B:302 , HOH B:450BINDING SITE FOR RESIDUE MG B 202
7AC7SOFTWAREVAL B:116 , LYS B:120 , SER B:123 , TRP B:124 , ASP B:125 , ALA B:127 , VAL B:129 , VAL B:158 , HOH B:346 , HOH B:460BINDING SITE FOR RESIDUE 1PE B 203
8AC8SOFTWAREASN B:29 , GLU B:81 , ARG B:84 , ASP B:114 , TRP B:115 , GLN B:118BINDING SITE FOR RESIDUE 1PE B 204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RKF)

(-) 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:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhh..hhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rkf A  16 QNFDYMFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGLERYRTITTAYYRGAMGFILMYDVTNEDSFNSVQDWVTQIKTYSWDNAQVILVGNKCDMEDQRVISFERGRQLADQLGVEFFETSAKENVNVKAVFERLVDIICDKM 186
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185 


Chain B from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..hhhhhhhhhh......eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhh..hhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rkf B  16 QNFDYMFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGLERYRTITTAYYRGAMGFILMYDVTNEDSFNSVQDWVTQIKTYSWDNAQVILVGNKCDMEDQRVISFERGRQLADQLGVEFFETSAKENVNVKAVFERLVDIICDKMS 187
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185
   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 4RKF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

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
    1PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GNP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4rkf)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 ](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
  4rkf
    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
  RAB3_DROME | P25228
    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
  RAB3_DROME | P25228
    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 4RKF)

(-) Related Entries Specified in the PDB File

1zbd 3rab 4rke