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 :  1.6A CRYSTAL STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN-III (PAP-III) WITH METHYLATED LYSINES
 
Authors :  I. V. Kurinov, F. M. Uckun
Date :  29 Apr 02  (Deposition) - 17 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Pokeweed Antiviral Protein, Ribosome Inactivating Protein, Polynucleotide:Adenosine, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. V. Kurinov, F. M. Uckun
High Resolution X-Ray Structure Of Potent Anti-Hiv Pokeweed Antiviral Protein-Iii
Biochem. Pharm. V. 65 1709 2003
PubMed-ID: 12754107  |  Reference-DOI: 10.1016/S0006-2952(03)00144-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTIVIRAL PROTEIN 3
    ChainsA
    EC Number3.2.2.22
    Organism CommonAMERICAN POKEWEED
    Organism ScientificPHYTOLACCA AMERICANA
    Organism Taxid3527
    Other DetailsLATE SUMMER LEAVES
    SynonymPAP-II, RIBOSOME-INACTIVATING PROTEIN, RRNA N- GLYCOSIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric/Biological Unit (1, 14)
No.NameCountTypeFull Name
1MLY14Mod. Amino AcidN-DIMETHYL-LYSINE

(-) Sites  (0, 0)

(no "Site" information available for 1LLN)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:32 -A:259
2A:81 -A:98

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:44 -Pro A:45

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LLN)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RIP2_PHYAM192-208  1A:167-183

(-) Exons   (0, 0)

(no "Exon" information available for 1LLN)

(-) 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:262
 aligned with RIP2_PHYAM | Q40772 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:262
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285  
           RIP2_PHYAM    26 NIVFDVENATPETYSNFLTSLREAVKDKKLTCHGMIMATTLTEQPKYVLVDLKFGSGTFTLAIRRGNLYLEGYSDIYNGKCRYRIFKDSESDAQETVCPGDKSKPGTQNNIPYEKSYKGMESKGGARTKLGLGKITLKSRMGKIYGKDATDQKQYQKNEAEFLLIAVQMVTEASRFKYIENKVKAKFDDANGYQPDPKAISLEKNWDSVSKVIAKVGTSGDSTVTLPGDLKDENNKPWTTATMNDLKNDIMALLTHVTCKVK 287
               SCOP domains d1llna_ A: Antiviral protein 3                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1llnA01 A:1-175 Ricin (A subunit), domain 1                                                                                                                                    1llnA02 A:176-262 Ricin (A Subunit), domain 2                                           CATH domains
               Pfam domains --RIP-1llnA01 A:3-216                                                                                                                                                                                                   ---------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhhhheeeeeee..eeee........eeeeeeee..eeeeeeee.....eeeeeeee..eeeee.......hhhhhhh.................hhhhhhhhhhhhhhh..hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh......eee..............eeehhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lln A   1 NIVFDVENATPETYSNFLTSLREAVkDkKLTCHGMIMATTLTEQPkYVLVDLkFGSGTFTLAIRRGNLYLEGYSDIYNGKCRYRIFkDSESDAQETVCPGDKSKPGTQNNIPYEkSYKGMESKGGARTKLGLGkITLKSRMGkIYGKDATDQKQYQKNEAEFLLIAVQMVTEASRFkYIENkVkAKFDDANGYQPDPkAISLEKNWDSVSkVIAKVGTSGDSTVTLPGDLkDENNKPWTTATMNDLKNDIMALLTHVTCKVK 262
                                    10        20     | |30        40     |  50  |     60        70        80      | 90       100       110    |  120       130   |   140  |    150       160       170      |180 | |   190       200       210|      220       230|      240       250       260  
                                                    26-MLY              46-MLY 53-MLY                            87-MLY                     115-MLY            134-MLY  143-MLY                           177-MLY| |           198-MLY      211-MLY             231-MLY                           
                                                      28-MLY                                                                                                                                                   182-MLY                                                                            
                                                                                                                                                                                                                 184-MLY                                                                          

   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

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RIP2_PHYAM | Q40772)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0030598    rRNA N-glycosylase activity    Catalysis of the hydrolysis of the N-glycosylic bond at A-4324 in 28S rRNA from rat ribosomes or corresponding sites in 28S RNA from other species.
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.

 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
    MLY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1lln)
 
  Cis Peptide Bonds
    Gln A:44 - Pro A:45   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1lln
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RIP2_PHYAM | Q40772
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.2.2.22
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  RIP2_PHYAM | Q40772
    Protein Disorder PredictionDisEMBL | 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 1LLN)

(-) Related Entries Specified in the PDB File

1qcg LOW TEMPERATURE STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN, WILD-TYPE ISOFORM (PAP-I)