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 :  STRUCTURE OF MUTANT RIP FROM BARLEY SEEDS IN COMPLEX WITH ADENINE
 
Authors :  B. -G. Lee, M. K. Kim, S. W. Suh, H. K. Song
Date :  22 May 12  (Deposition) - 31 Oct 12  (Release) - 23 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
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 :  Hydrolase, Ribosome Inactivating Protein, Rrna N-Glycosylase Activity, Ribosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. G. Lee, M. K. Kim, B. W. Kim, S. W. Suh, H. K. Song
Structures Of The Ribosome-Inactivating Protein From Barley Seeds Reveal A Unique Activation Mechanism.
Acta Crystallogr. , Sect. D V. 68 1488 2012
PubMed-ID: 23090398  |  Reference-DOI: 10.1107/S0907444912037110

(-) Compounds

Molecule 1 - PROTEIN SYNTHESIS INHIBITOR I
    Chains: A, B, C, D
    EC Number: 3.2.2.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RIP30
    Mutation: YES
    Organism Common: BARLEY
    Organism Scientific: HORDEUM VULGARE
    Organism Taxid: 4513
    Synonym: RIBOSOME-INACTIVATING PROTEIN I, RRNA N-GLYCOSIDASE

 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, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1ADE4Ligand/IonADENINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ADE1Ligand/IonADENINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ADE1Ligand/IonADENINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1ADE1Ligand/IonADENINE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1ADE1Ligand/IonADENINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:86 , TYR A:87 , LEU A:88 , GLY A:116 , TYR A:118 , LEU A:170 , ARG A:178 , HOH A:419BINDING SITE FOR RESIDUE ADE A 301
2AC2SOFTWAREILE B:86 , TYR B:87 , LEU B:88 , GLY B:116 , TYR B:118 , LEU B:170 , ARG B:178 , HOH B:429BINDING SITE FOR RESIDUE ADE B 301
3AC3SOFTWAREILE C:86 , TYR C:87 , LEU C:88 , GLY C:116 , TYR C:118 , LEU C:170 , GLU C:175 , ARG C:178 , HOH C:402BINDING SITE FOR RESIDUE ADE C 301
4AC4SOFTWAREILE D:86 , TYR D:87 , LEU D:88 , GLY D:116 , LEU D:170 , ARG D:178 , HOH D:614 , HOH D:714BINDING SITE FOR RESIDUE ADE D 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FBA)

(-) 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:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhhhhhhhhhhh....ee..ee.............eeeeeee.......eeeeee.....eeeee.....eee.........ee.....hhhhhhh..hhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeehhhhhhhhhhhhhhhhhhhhh...............hhhhh..hhhhhhhhh............hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fba A   4 KMAKNVDKPLFTATFNVQASSADYATFIAGIRNKLRNPAHFSHNRPVLPPVEPNVPPSRWFHVVLKASPTSAGLTLAIRADNIYLEGFKSSDGTWWELTPGLIPGATYVGFGGTYRDLLGDTDKLTNVALGRQQLADAVTALHGRTKADKPSGPKQQQAREAVTTLLLMVNEATRFQTVSGFVAGLLHPKAVAAASGKIGNEMKAQVNGWQDLSAALLKTDVKPPPGKSPAKFAPIEKMGVRTAVQAANTLGILLFVEVPGGLTVAKALELFHASGGK 281
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273        


Chain B from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhhhhhhhhhhh....ee..ee.............eeeeeee.......eeeeee.....eeeee.....eee.........ee.....hhhhhhh..hhhhhh.eehhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeehhhhhhhhhhhhhhhhhhhhhhh.............hhhhh..hhhhhhhhh............hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fba B   4 KMAKNVDKPLFTATFNVQASSADYATFIAGIRNKLRNPAHFSHNRPVLPPVEPNVPPSRWFHVVLKASPTSAGLTLAIRADNIYLEGFKSSDGTWWELTPGLIPGATYVGFGGTYRDLLGDTDKLTNVALGRQQLADAVTALHGRTKADKPSGPKQQQAREAVTTLLLMVNEATRFQTVSGFVAGLLHPKAVAAASGKIGNEMKAQVNGWQDLSAALLKTDVKPPPGKSPAKFAPIEKMGVRTAVQAANTLGILLFVEVPGGLTVAKALELFHASGGK 281
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273        


Chain C from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhhhhhhhhhhh....ee..ee.............eeeeeee.......eeeeee.....eeeee.....eee.........ee.....hhhhhh.hhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhh...............hhhhh..hhhhhhhhh............hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fba C   4 KMAKNVDKPLFTATFNVQASSADYATFIAGIRNKLRNPAHFSHNRPVLPPVEPNVPPSRWFHVVLKASPTSAGLTLAIRADNIYLEGFKSSDGTWWELTPGLIPGATYVGFGGTYRDLLGDTDKLTNVALGRQQLADAVTALHGRTKADKPSGPKQQQAREAVTTLLLMVNEATRFQTVSGFVAGLLHPKAVAAASGKIGNEMKAQVNGWQDLSAALLKTDVKPPPGKSPAKFAPIEKMGVRTAVQAANTLGILLFVEVPGGLTVAKALELFHASGGK 281
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273        


Chain D from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhhhhhhhhhhh....ee..ee.............eeeeeee.......eeeeee.....eeeee.....eee.........ee.....hhhhhhhhhhhhhhh.eehhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........ee..hhhhhhhhhhhhhhhhhhhhhhh.............hhhhh..hhhhhhhhh............hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fba D   4 KMAKNVDKPLFTATFNVQASSADYATFIAGIRNKLRNPAHFSHNRPVLPPVEPNVPPSRWFHVVLKASPTSAGLTLAIRADNIYLEGFKSSDGTWWELTPGLIPGATYVGFGGTYRDLLGDTDKLTNVALGRQQLADAVTALHGRTKADKPSGPKQQQAREAVTTLLLMVNEATRFQTVSGFVAGLLHPKAVAAASGKIGNEMKAQVNGWQDLSAALLKTDVKPPPGKSPAKFAPIEKMGVRTAVQAANTLGILLFVEVPGGLTVAKALELFHASGGK 281
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273
   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 4FBA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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
    ADE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4fba)
 
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
  4fba
    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
  RIP1_HORVU | P22244
    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)
  3.2.2.22
    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
  RIP1_HORVU | P22244
    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
        RIP1_HORVU | P22244: 4fb9 4fbb 4fbc 4fbh

(-) Related Entries Specified in the PDB File

4fb9 4fbb 4fbc 4fbh