Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
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 N-ACETYLGLUCOSAMINE AT 1.62 A RESOLUTION
 
Authors :  S. Yamini, S. Pandey, M. Sinha, P. Kaur, S. Sharma, T. P. Singh
Date :  25 Feb 12  (Deposition) - 07 Mar 12  (Release) - 07 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.62
Chains :  Asym./Biol. Unit :  A
Keywords :  Rip, Plant Protein, N-Acetylglucosamine, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Yamini, S. Pandey, M. Sinha, P. Kaur, S. Sharma, T. P. Singh
Crystal Structure Of The Complex Of Type I Ribosome Inactivating Protein With N-Acetylglucosamine At 1. 62 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RRNA N-GLYCOSIDASE
    Chains: A
    EC Number: 3.2.2.22
    Organism Common: BITTER GOURD
    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  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:226 , ASN A:227 , THR A:229 , HOH A:497 , HOH A:662 , HOH A:663BINDING SITE FOR RESIDUE NAG A 301
2AC2SOFTWARELEU A:6 , ALA A:9 , ARG A:101 , ILE A:103 , PRO A:130 , ALA A:175 , HOH A:452 , HOH A:507BINDING SITE FOR RESIDUE GOL A 302
3AC3SOFTWAREASN A:33 , THR A:234 , SER A:235 , GLN A:238 , HOH A:595BINDING SITE FOR RESIDUE GOL A 303
4AC4SOFTWAREVAL A:69 , TYR A:70 , ILE A:71 , GLY A:109 , ASN A:110 , TYR A:111 , ILE A:155 , ALA A:159 , ARG A:163 , HOH A:673 , HOH A:674 , HOH A:675BINDING SITE FOR RESIDUE NAG A 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4DWM)

(-) 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
 aligned with D9J2T9_MOMBA | D9J2T9 from UniProtKB/TrEMBL  Length:246

    Alignment length: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      
         D9J2T9_MOMBA     1 DVSFRLSGADPSSYGMFIKDLRNALPHTEKVYNIPLLLPSVSGAGRYLLMHLFNYDGNTITVAVDVTNVYIMGYLALTTSYFFNEPAADLASQYVFRSARRKITLPYSGNYERLQIAAGKPREKIPIGLPALDTAISTLLHYDSTAAAGALLVLIQTTAEAARFKYIEQQIQERAYRDEVPSSATISLENSWSGLSKQIQLAQGNNGVFRTPTVLVDSKGNRVQITNVTSNVVTSNIQLLLNTKNI 246
               SCOP domains d4dwma_ 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..hhhhhhhh........eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeee..hhhhhh......hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dwm A   1 DVSFRLSGADPSSYGMFIKDLRNALPHTEKVYNIPLLLPSVSGAGRYLLMHLFNYDGNTITVAVDVTNVYIMGYLALTTSYFFNEPAADLASQYVFRSARRKITLPYSGNYERLQIAAGKPREKIPIGLPALDTAISTLLHYDSTAAAGALLVLIQTTAEAARFKYIEQQIQERAYRDEVPSSATISLENSWSGLSKQIQLAQGNNGVFRTPTVLVDSKGNRVQITNVTSNVVTSNIQLLLNTKNI 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 4DWM)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (D9J2T9_MOMBA | D9J2T9)
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: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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ 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 4dwm)
 

(-) 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
  4dwm
    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
  D9J2T9_MOMBA | D9J2T9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  D9J2T9_MOMBA | D9J2T9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        D9J2T9_MOMBA | D9J2T9: 3mrw 3n1n 3n2d 3n31 3n3x 3n5d 3nfm 3njs 3nx9 3q4p 3qji 3rl9 3s9q 3sj6 3u6t 3u6z 3u70 3u8f 3v14 3v2k 4emf 4emr 4f9n 4fxa 4fz9 4guw 4h0z 4hoa 4i47 4jtb 4jtp 4k2z 4k6p 4k6s 4kl4 4kmk 4kpv 4kwn 4l66 4lro 4lt4 4lwx 4m5a 4o0o 4o4q 4o8e 4q9f 4qgj 4rzj 4xy7 4zt8 4zu0 4zw4 4zz6 5cix 5cso 5cst 5gm7 5gz7 5ilw 5ilx 5wv1

(-) Related Entries Specified in the PDB File

3mrw