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(-) Description

Title :  STRUCTURAL STUDIES ON A NON-TOXIC HOMOLOGUE OF TYPE II RIPS FROM MOMORDICA CHARANTIA (BITTER GOURD)-NATIVE-2
 
Authors :  T. Chandran, A. Sharma, M. Vijayan
Date :  12 Apr 15  (Deposition) - 23 Mar 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
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  (4, 18)

Asymmetric/Biological Unit (4, 18)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2EDO11Ligand/Ion1,2-ETHANEDIOL
3FUC1Ligand/IonALPHA-L-FUCOSE
4NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:15 , GLN A:169 , ILE B:142 , GLY B:143 , EDO B:315 , HOH B:456 , HOH B:460binding site for residue EDO A 302
02AC2SOFTWAREASN A:109 , THR A:110 , PHE A:111 , HOH A:401 , HOH A:439 , HOH A:510binding site for residue EDO A 303
03AC3SOFTWARETYR B:80 , NAG B:301binding site for residue NAG B 302
04AC4SOFTWARENAG B:305binding site for residue BMA B 306
05AC5SOFTWARELYS B:199 , HOH B:408 , HOH B:600binding site for residue EDO B 307
06AC6SOFTWAREGLU A:192 , TYR A:218 , ALA B:234 , GLN B:235 , HOH B:407 , HOH B:645binding site for residue EDO B 308
07AC7SOFTWAREMET B:147 , LEU B:160 , GLU B:161 , VAL B:238 , TYR B:239 , LYS B:241binding site for residue EDO B 309
08AC8SOFTWAREARG B:16 , ASP B:17 , CYS B:206 , ASP B:207 , GLY B:208 , HOH B:435binding site for residue EDO B 310
09AC9SOFTWARETHR A:121 , SER A:123 , GLU A:124 , ASP B:237 , TYR B:239 , HOH B:406 , HOH B:510binding site for residue EDO B 311
10AD1SOFTWAREGLN B:8 , ARG B:9 , THR B:10 , HOH B:419binding site for residue EDO B 312
11AD2SOFTWAREASP B:22 , TYR B:24 , GLY B:25 , ASN B:44 , HOH B:420 , HOH B:593binding site for residue EDO B 313
12AD3SOFTWAREARG B:12 , GLN B:41 , ASN B:132 , ASP B:195 , SER B:196 , SER B:197 , HOH B:540 , HOH B:555binding site for residue EDO B 314
13AD4SOFTWAREEDO A:302 , GLY B:143 , LEU B:144 , ARG B:145 , HIS B:146 , HOH B:460 , HOH B:545binding site for residue EDO B 315
14AD5SOFTWAREASN A:87 , ASN A:108 , HOH A:408 , LYS B:251 , HOH B:495binding site for Mono-Saccharide NAG A 301 bound to ASN A 108
15AD6SOFTWARELEU B:62 , ALA B:63 , THR B:64 , LEU B:67 , LEU B:81 , ASP B:84 , TRP B:87 , ASN B:97 , NAG B:302 , HOH B:432 , HOH B:445binding site for Mono-Saccharide NAG B 301 bound to ASN B 97
16AD7SOFTWAREGLU A:124 , PRO A:126 , HIS A:131 , ARG B:33 , ASN B:72 , ASN B:114 , BMA B:306 , HOH B:401 , HOH B:412 , HOH B:424 , HOH B:475 , HOH B:519binding site for Poly-Saccharide residues NAG B 303 through NAG B 305

(-) 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 4Z9W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z9W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z9W)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z9W)

(-) 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..eeeee.....hhhhh.....eeeee....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee.....eeeeee..hhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z9w 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.....eee..........eee....hhhhh.ee......eeeeeehhhhheeeee....eeeee.....hhhh.eee.....eee..eeeeeee..........eeee...hhhhh.ee.....eee....eeeee.hhhhhhh.eeee...........eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z9w 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)
  - → 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  (0, 0)

(no "SCOP Domain" information available for 4Z9W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z9W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z9W)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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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 4za3 4zbv 4zfu 4zfw 4zfy 4zgr 4zlb

(-) Related Entries Specified in the PDB File

4z8s THE SAME PROTEIN IN DIFFERENT NATIVE FORM (NATIVE I)