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(-) Description

Title :  STRUCTURAL STUDIES ON A NON-TOXIC HOMOLOGUE OF TYPE II RIPS FROM MOMORDICA CHARANTIA (BITTER GOURD) IN COMPLEX WITH BENZYL T-ANTIGEN
 
Authors :  T. Chandran, A. Sharma, M. Vijayan
Date :  15 Apr 15  (Deposition) - 23 Mar 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Trefoil, Type Ii Rips, Galactose Specific Lectin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Chandran, A. Sharma, M. Vijayan
Structural Studies On A Non-Toxic Homologue Of Type Ii Rips From Bitter Gourd: Molecular Basis Of Non-Toxicity, Conformational Selection And Glycan Structure.
J. Biosci. V. 40 929 2015
PubMed-ID: 26648038
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RRNA N-GLYCOSIDASE
    Chains: A
    EC Number: 3.2.2.22
    Fragment: UNP RESIDUES 24-270
    Organism Common: BITTER GOURD
    Organism Scientific: MOMORDICA CHARANTIA
    Organism Taxid: 3673
 
Molecule 2 - RRNA N-GLYCOSIDASE
    Chains: B
    EC Number: 3.2.2.22
    Fragment: UNP RESIDUES 287-547
    Organism Common: BITTER GOURD
    Organism Scientific: MOMORDICA CHARANTIA
    Organism Taxid: 3673

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 13)

Asymmetric/Biological Unit (9, 13)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2BMA1Ligand/IonBETA-D-MANNOSE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4FUC1Ligand/IonALPHA-L-FUCOSE
5GAL1Ligand/IonBETA-D-GALACTOSE
6MBN1Ligand/IonTOLUENE
7NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
8PGE1Ligand/IonTRIETHYLENE GLYCOL
9PO41Ligand/IonPHOSPHATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:86 , ASN A:108 , HOH A:467binding site for residue NAG A 301
02AC2SOFTWAREILE A:45 , ARG A:48 , PRO A:89 , PRO A:90 , ILE A:91binding site for residue PO4 A 302
03AC3SOFTWARENAG B:301 , FUC B:302 , BMA B:306 , HOH B:522binding site for residue NAG B 303
04AC4SOFTWARENAG B:303 , HOH B:537binding site for residue BMA B 306
05AC5SOFTWAREASN B:183 , ASN B:184 , ASN B:185 , ARG B:186 , PGE B:308binding site for residue EDO B 307
06AC6SOFTWAREVAL B:138 , ASN B:183 , EDO B:307 , HOH B:481binding site for residue PGE B 308
07AC7SOFTWAREASP A:58 , ASP B:22 , VAL B:23 , TYR B:24 , GLY B:25 , TYR B:37 , GLN B:42 , ASN B:44 , A2G B:310binding site for residue GAL B 309
08AC8SOFTWAREALA B:63 , THR B:64 , LEU B:67 , LEU B:81 , ASP B:84 , TRP B:87 , ASN B:97 , SER B:100 , HOH B:441binding site for Poly-Saccharide residues NAG B 304 through NAG B 305 bound to ASN B 97
09AC9SOFTWARETYR A:146 , ARG B:33 , ASN B:72 , ASN B:114 , NAG B:303 , HOH B:464 , HOH B:484binding site for Poly-Saccharide residues NAG B 301 through FUC B 302 bound to ASN B 114
10AD1SOFTWARESER A:5 , GLN A:6 , SER A:7 , ASN A:56 , GLY A:57 , ASN A:59 , GLU A:133 , GLY B:25 , GAL B:309binding site for Poly-Saccharide residues A2G B 310 through MBN B 311

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:46 -A:46
2A:246 -B:4
3B:20 -B:39
4B:61 -B:78
5B:148 -B:163
6B:189 -B:206

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZBV)

(-) 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:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhhhhhhhhhhhhhhhhhh.................hhhh.eeeeeee.....eeeeeee....eeeeeee..eeee......hhhhh.....eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.....eeeeee..hhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zbv A   1 NLSLSQSNFSADTYKSFIKNLRKQLTIGASYGSAGIPILKHSVPICERFLLVDLTNGDNETITLAINVEDAGFAAYRAADRSYFFQNAPPIASYVIFTDTNQNIMNFNNTFESIEIVGGTTRSETPLGIMHFEASIFHLFVHDENYVPTSFLVLIQMVLEAAKFKFIEQKVIHSIMDMEDFTPGLAMLSLEENWTQLSLQLQASESLNGVFGDSVSLYNSMDEPIGVDSMYYPILTANMAFQLYQCP 247
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       


Chain B from PDB  Type:PROTEIN  Length:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...eee.eehhhhheeee.hhh....eeeeee....hhhhheee.....eee..eeeee........eeeehhhhhh....eee.....eee....eeeee........eeeee...hhhhh.ee......eeeeeehhh.eeeeee....eeeeee....hhhh.eee.....eee..eeeeeee..........eeee...hhhhh.ee.....eee....eeeee.hhhhhhh.eeee...........eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zbv B   1 NEQCSPQQRTTRISGRDGLCVDVYGALTADGSRVILYPCGQQQNQQWTFYPDNTIRSLGKCLATSALSSGSNVVITNCDYLRYDDGWMVSSSGTMMNKSSHLVLTANAATSRTNLTGENNVFAAKQAWRIGNYVEPIVTTIIGLRHMCLEATDNDTNVWLESCVKNKTKQYWALYSDDTIRVNNNRNLCVSSSTDSSSKLIVIRRCDGSINQRWVFTPQGTISNPGYEAVMDVAQNDVYLKKIVLSSATDKGNGQQWTVFY 261
                                    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
   Legend:   → Mismatch (orange background)
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  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 4ZBV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        B7X8M2_MOMCH | B7X8M2: 4z8s 4z9w 4za3 4zfu 4zfw 4zfy 4zgr 4zlb

(-) Related Entries Specified in the PDB File

4za3 SAME PROTEIN IN ITS NATIVE FORM