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(-) Description

Title :  STRUCTURAL STUDIES ON A NON-TOXIC HOMOLOGUE OF TYPE II RIPS FROM MOMORDICA CHARANTIA (BITTER GOURD)-NATIVE-3
 
Authors :  T. Chandran, A. Sharma, M. Vijayan
Date :  13 Apr 15  (Deposition) - 23 Mar 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
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 288-547
    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  (5, 14)

Asymmetric/Biological Unit (5, 14)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2EDO6Ligand/Ion1,2-ETHANEDIOL
3FUC1Ligand/IonALPHA-L-FUCOSE
4GOL1Ligand/IonGLYCEROL
5NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:109 , THR A:110 , PHE A:111 , ILE A:155 , HOH A:402 , HOH A:403 , HOH A:410 , HOH A:501binding site for residue EDO A 301
02AC2SOFTWAREHIS A:131 , ALA A:134 , SER A:135 , HIS A:138 , SER A:150 , HOH B:562binding site for residue EDO A 302
03AC3SOFTWAREGLN B:8 , ARG B:9 , THR B:10binding site for residue EDO B 301
04AC4SOFTWAREARG B:16 , ASP B:17 , ALA B:109 , SER B:111 , CYS B:206 , ASP B:207 , HOH B:404 , HOH B:463binding site for residue EDO B 302
05AC5SOFTWAREASP A:222 , LYS B:242 , HOH B:409 , HOH B:589binding site for residue EDO B 303
06AC6SOFTWAREGLY B:143 , LEU B:144 , ARG B:145 , HIS B:146 , HOH B:415 , HOH B:504 , HOH B:553 , HOH B:600binding site for residue EDO B 304
07AC7SOFTWAREMET A:178 , ASP B:22 , TYR B:24 , GLY B:25 , GLN B:42 , ASN B:44 , HOH B:427 , HOH B:628binding site for residue GOL B 311
08AC8SOFTWAREGLN A:86 , ASN A:108 , HOH A:445 , HOH A:453binding site for Mono-Saccharide NAG A 303 bound to ASN A 108
09AC9SOFTWAREALA 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:426 , HOH B:462binding site for Poly-Saccharide residues NAG B 309 through NAG B 310 bound to ASN B 97
10AD1SOFTWAREGLU A:124 , PRO A:126 , HIS A:131 , ARG B:33 , ASN B:72 , ASN B:114 , NAG B:307 , HOH B:410 , HOH B:416 , HOH B:420 , HOH B:473binding site for Poly-Saccharide residues NAG B 305 through FUC B 306 bound to ASN B 114
11AD2SOFTWARENAG B:305binding site for Poly-Saccharide residues NAG B 307 through BMA B 308

(-) 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 4ZA3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZA3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZA3)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZA3)

(-) 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.....eeeeee..eeee......hhhhh.....eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.....eeeeee..hhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4za3 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:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.eehhhhheeee.hhh....eeeeee....hhhhheee.....eee..eeeee........eeeehhhhhh....eee.....eee.....eee..........eee....hhhhh.ee......eeeeeehhhhheeeee....eeeee.....hhhh.eee.....eee.....eeee..........eeee...hhhhh.ee.....eee....eeeee.hhhhhhh.eeee...........eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4za3 B   2 EQCSPQQRTTRISGRDGLCVDVYGALTADGSRVILYPCGQQQNQQWTFYPDNTIRSLGKCLATSALSSGSNVVITNCDYLRYDDGWMVSSSGTMMNKSSHLVLTANAATSRTNLTGENNVFAAKQAWRIGNYVEPIVTTIIGLRHMCLEATDNDTNVWLESCVKNKTKQYWALYSDDTIRVNNNRNLCVSSSTDSSSKLIVIRRCDGSINQRWVFTPQGTISNPGYEAVMDVAQNDVYLKKIVLSSATDKGNGQQWTVFY 261
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261
   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 4ZA3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZA3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZA3)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  4za3
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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 4zbv 4zfu 4zfw 4zfy 4zgr 4zlb

(-) Related Entries Specified in the PDB File

4z8s THE SAME PROTEIN IN NATIVE FORM (NATIVE I) SOAKED IN GLYCEROL
4z9w