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(-) Description

Title :  CRYSTAL STRUCTURE OF CYANOVIRIN-N COMPLEXED TO A SYNTHETIC HEXAMANNOSIDE
 
Authors :  I. Botos, B. R. O'Keefe, S. R. Shenoy, P. H. Seeberger, M. R. Boyd, A. Wlod
Date :  03 Apr 09  (Deposition) - 05 May 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cyanovirin-N, Hiv-Inactivating, Domain-Swapping, Gp120, Man-9, Oligosaccharide, Antiviral Protein, Disulfide Bond, Protein Synthesis Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Botos, B. R. O'Keefe, S. R. Shenoy, L. K. Cartner, D. M. Ratner, P. H. Seeberger, M. R. Boyd, A. Wlodawer
Structures Of The Complexes Of A Potent Anti-Hiv Protein Cyanovirin-N And High Mannose Oligosaccharides
J. Biol. Chem. V. 277 34336 2002
PubMed-ID: 12110688  |  Reference-DOI: 10.1074/JBC.M205909200

(-) Compounds

Molecule 1 - CYANOVIRIN-N
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: NOSTOC ELLIPSOSPORUM
    Organism Taxid: 45916
    Synonym: CV-N

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1MAN4Ligand/IonALPHA-D-MANNOSE
2MG1Ligand/IonMAGNESIUM ION
3NHE1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
4OPM2Ligand/IonO1-PENTYL-MANNOSE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:25 , HOH A:149 , MAN A:504BINDING SITE FOR RESIDUE OPM A 503
2AC2SOFTWAREGLU A:23 , ARG A:24 , THR A:25 , OPM A:503 , MAN A:505 , ASN B:93 , ILE B:94 , ASP B:95BINDING SITE FOR RESIDUE MAN A 504
3AC3SOFTWAREGLY A:2 , LYS A:3 , PHE A:4 , GLN A:6 , THR A:7 , MAN A:504 , ALA B:92 , ASN B:93BINDING SITE FOR RESIDUE MAN A 505
4AC4SOFTWARELYS A:48 , TRP A:49 , ASN A:53 , ARG A:76 , HOH A:129 , HOH A:150 , HOH A:152 , ASN B:42 , ASP B:44BINDING SITE FOR RESIDUE NHE A 301
5AC5SOFTWARESER A:38 , GLN A:50 , HOH A:107 , SER B:38 , GLN B:50 , HOH B:113BINDING SITE FOR RESIDUE MG A 102
6AC6SOFTWAREGLU B:23 , THR B:25 , GLY B:27 , HOH B:103 , MAN B:604BINDING SITE FOR RESIDUE OPM B 603
7AC7SOFTWAREASN A:93 , ASP A:95 , THR B:7 , GLU B:23 , ARG B:24 , THR B:25 , OPM B:603 , MAN B:605BINDING SITE FOR RESIDUE MAN B 604
8AC8SOFTWAREALA A:92 , ASN A:93 , GLY B:2 , LYS B:3 , PHE B:4 , THR B:7 , MAN B:604BINDING SITE FOR RESIDUE MAN B 605

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:8 -A:22
2A:58 -A:73
3B:8 -B:22
4B:58 -B:73

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GXY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GXY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GXY)

(-) Exons   (0, 0)

(no "Exon" information available for 3GXY)

(-) 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:101
 aligned with CVN_NOSEL | P81180 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:101
                                    10        20        30        40        50        60        70        80        90       100 
            CVN_NOSEL     1 LGKFSQTCYNSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKWQPSNFIETCRNTQLAGSSELAAECKTRAQQFVSTKINLDDHIANIDGTLKYE 101
               SCOP domains d3gxya_ A: Cyanovirin-N                                                                               SCOP domains
               CATH domains 3gxyA00 A:1-101 HIV-inactivating Protein,Cyanovirin-n;                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhh.eeeeeee..eeeeeee.....eeeeeee....eeee..eeee...hhhhheeeeeee...eeeeeee.....eeeeeee....eee....eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 3gxy A   1 LGKFSQTCYNSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKWQPSNFIETCRNTQLAGSSELAAECKTRAQQFVSTKINLDDHIANIDGTLKYE 101
                                    10        20        30        40        50        60        70        80        90       100 


Chain B from PDB  Type:PROTEIN  Length:101
 aligned with CVN_NOSEL | P81180 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:101
                                    10        20        30        40        50        60        70        80        90       100 
            CVN_NOSEL     1 LGKFSQTCYNSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKWQPSNFIETCRNTQLAGSSELAAECKTRAQQFVSTKINLDDHIANIDGTLKYE 101
               SCOP domains d3gxyb_ B: Cyanovirin-N                                                                               SCOP domains
               CATH domains 3gxyB00 B:1-101 HIV-inactivating Protein,Cyanovirin-n;                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhh.eeeeeee..eeeeeee.....eeeeeee....eeee..eeee...hhhhheeeeeee...eeeeeee.....eeeeeee....eeee..eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 3gxy B   1 LGKFSQTCYNSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKWQPSNFIETCRNTQLAGSSELAAECKTRAQQFVSTKINLDDHIANIDGTLKYE 101
                                    10        20        30        40        50        60        70        80        90       100
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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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GXY)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CVN_NOSEL | P81180)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
biological process
    GO:0050688    regulation of defense response to virus    Any process that modulates the frequency, rate or extent of the antiviral response of a cell or organism.

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  3gxy
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 Related Entries

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

UniProtKB/Swiss-Prot
        CVN_NOSEL | P81180: 1iiy 1j4v 1l5b 1l5e 1lom 1n02 2ezm 2ezn 2pys 2rdk 2rp3 2z21 3czz 3ezm 3gxz 3lhc 3s3y 3s3z 4j4c 4j4d 4j4e 4j4f 4j4g

(-) Related Entries Specified in the PDB File

1m5j THE SAME PROTEIN COMPLEXED TO SYNTHETIC HEXAMANNOSE
1m5m THE SAME PROTEIN COMPLEXED WITH MAN-9
3gxz