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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 N-ACETYL D GALACTOSAMINE
 
Authors :  T. Chandran, A. Sharma, M. Vijayan
Date :  21 Apr 15  (Deposition) - 23 Mar 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.53
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Trefoil, Type Ii Rips, Galactose Binding 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  (7, 12)

Asymmetric/Biological Unit (7, 12)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2BMA1Ligand/IonBETA-D-MANNOSE
3FUC1Ligand/IonALPHA-L-FUCOSE
4GOL2Ligand/IonGLYCEROL
5NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
6PGE1Ligand/IonTRIETHYLENE GLYCOL
7XYP1Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:42 , ARG A:48 , THR A:98 , HOH A:471binding site for residue GOL A 301
2AC2SOFTWAREASP A:70 , GLY A:72 , ASN A:109 , PHE A:111 , GLU A:160 , LYS A:163 , GLU A:191 , TRP A:194binding site for residue PGE A 303
3AC3SOFTWAREGLY A:57 , ASP A:58 , ASP B:22 , VAL B:23 , GLY B:25 , TYR B:37 , GLN B:42 , ASN B:44 , ARG B:112 , GOL B:302 , HOH B:475binding site for residue A2G B 301
4AC4SOFTWAREGLY A:57 , ASN A:59 , A2G B:301binding site for residue GOL B 302
5AC5SOFTWAREASN A:108 , SER A:113 , HOH A:413binding site for Mono-Saccharide NAG A 302 bound to ASN A 108
6AC6SOFTWARELEU B:62 , ALA B:63 , THR B:64 , LEU B:67 , TYR B:80 , LEU B:81 , ASP B:84 , TRP B:87 , ASN B:97 , SER B:100 , HOH B:424binding site for Poly-Saccharide residues NAG B 303 through NAG B 304 bound to ASN B 97
7AC7SOFTWAREHIS A:131 , TYR A:146 , THR A:182 , ARG B:33 , ASN B:72 , ASN B:114binding site for Poly-Saccharide residues NAG B 305 through XYP B 309 bound to ASN B 114

(-) 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 4ZFU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZFU)

(-) 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...ee.....ee.....hhhh.eeeeeee.....eeeeeee.....eeeeee..eeeee.....hhhhh.....eeeee....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.....eeeeee..hhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zfu 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......eeeeeehhhhhh....eee.....eee....eeeee........eeeee...hhhhh.ee......eeeeeee...eeeeee....eeeeee....hhhh.eee.....eee.....eeee..........eeee...hhhhh.ee.....eee....eeeee.hhhhhhh.eeee...........eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zfu 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 4ZFU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  4zfu
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  3.2.2.22
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4z8s THE SAME PROTEIN IN NATIVE FORM
4zfw
4zfy