Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX OF TYPE I RIBOSOME INACTIVATING PROTEIN WITH RIBOSE AT 1.7A RESOLUTION
 
Authors :  N. Pandey, G. S. Kushwaha, M. Sinha, P. Kaur, C. Betzel, S. Sharma, T. P. S
Date :  15 May 10  (Deposition) - 23 Jun 10  (Release) - 23 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Rip, Rna N-Glycosidase, Plant Protein, Ribose, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Pandey, G. S. Kushwaha, M. Sinha, P. Kaur, C. Betzel, S. Sharma, T. P. Singh
Crystal Structure Of The Complex Of Type I Ribosome Inactivating Protein With Ribose At 1. 7A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBOSOME INACTIVATING PROTEIN
    Chains: A
    EC Number: 3.2.2.22
    Organism Common: BALSAM APPLE
    Organism Scientific: MOMORDICA BALSAMINA
    Organism Taxid: 3672

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4RIP1Ligand/IonRIBOSE(PYRANOSE FORM)

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:226 , ASN A:227 , THR A:229 , NAG A:248 , HOH A:296BINDING SITE FOR RESIDUE NAG A 247
2AC2SOFTWARENAG A:247BINDING SITE FOR RESIDUE NAG A 248
3AC3SOFTWARETYR A:70 , GLY A:109 , ASN A:110 , TYR A:111 , GLU A:160 , ARG A:163 , PEG A:251 , HOH A:263 , HOH A:439BINDING SITE FOR RESIDUE RIP A 249
4AC4SOFTWARELEU A:6 , ALA A:9 , ARG A:101 , ILE A:103 , ALA A:175 , HOH A:300 , HOH A:308BINDING SITE FOR RESIDUE GOL A 250
5AC5SOFTWAREVAL A:69 , TYR A:70 , ILE A:71 , PHE A:83 , GLU A:85 , GLY A:109 , ILE A:155 , ALA A:159 , RIP A:249 , HOH A:323BINDING SITE FOR RESIDUE PEG A 251

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N1D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3N1D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N1D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N1D)

(-) Exons   (0, 0)

(no "Exon" information available for 3N1D)

(-) 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:246
                                                                                                                                                                                                                                                                                      
               SCOP domains d3n1da_ A: automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhhh..eeeee..eeee....hhhh.eeeeeee.....eeeeeee.....eeeeee..eeee..hhhhhhhhh.......eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeee..hhhhhh......hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3n1d A   1 DVSFRLSGADPSSYGMFIKDLRNALPHTEKVYNIPLLLPSVSGAGRYLLMHLFNYDGNTITVAVDVTNVYIMGYLALTTSYFFNEPAADLASQYVFRSARRKITLPYSGNYERLQIAAGKPREKIPIGLPALDTAISTLLHYDSTAAAGALLVLIQTTAEAARFKYIEQQIQERAYRDEVPSSATISLENSWSGLSKQIQLAQGNNGVFRTPTVLVDSGGNRVQITNVTSNVVTSNIQLLLNTKNI 246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N1D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3N1D)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3N1D)

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    RIP  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3n1d)
 

(-) 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
  3n1d
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 3N1D)

(-) Related Entries Specified in the PDB File

1aha CRYSTAL STRUCTURES OF ALPHA-MOMORCHARIN