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(-) Description

Title :  FIVE SITE MUTATED CYANOVIRIN-N WITH MANNOSE DIMER BOUND
 
Authors :  R. Fromme, Z. Katiliene, P. Fromme, G. Ghirlanda
Date :  24 Sep 07  (Deposition) - 06 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cyanovirin-N, Sugar Binding Protein, Anti Hiv, X-Ray Diffraction, Antiviral Protein, Protein Synthesis Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Fromme, Z. Katiliene, P. Fromme, G. Ghirlanda
Conformational Gating Of Dimannose Binding To The Antiviral Protein Cyanovirin Revealed From The Crystal Structure At 1. 35 A Resolution.
Protein Sci. V. 17 939 2008
PubMed-ID: 18436959  |  Reference-DOI: 10.1110/PS.083472808
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYANOVIRIN-N
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: M51
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: NOSTOC ELLIPSOSPORUM
    Organism Taxid: 45916
    Synonym: CV-N

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MAN4Ligand/IonALPHA-D-MANNOSE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MAN2Ligand/IonALPHA-D-MANNOSE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MAN2Ligand/IonALPHA-D-MANNOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:42 , ASP A:44 , LYS A:74 , THR A:75 , ARG A:76 , GLN A:78 , HOH A:143 , HOH A:163 , HOH B:191BINDING SITE FOR RESIDUE MAN A 110
2AC2SOFTWAREGLU A:41 , ASN A:42 , SER A:52 , ASN A:53 , PHE A:54 , GLU A:56 , THR A:57 , HOH A:138 , HOH A:163 , HOH B:201BINDING SITE FOR RESIDUE MAN A 111
3AC3SOFTWAREASN B:42 , ASP B:44 , LYS B:74 , THR B:75 , ARG B:76 , GLN B:78 , HOH B:179 , HOH B:253BINDING SITE FOR RESIDUE MAN B 110
4AC4SOFTWAREGLU B:41 , ASN B:42 , SER B:52 , ASN B:53 , PHE B:54 , GLU B:56 , THR B:57 , HOH B:169BINDING SITE FOR RESIDUE MAN B 111

(-) SS Bonds  (4, 4)

Asymmetric 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 2RDK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RDK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RDK)

(-) Exons   (0, 0)

(no "Exon" information available for 2RDK)

(-) Sequences/Alignments

Asymmetric 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
                                                                                                                             101 
                                    11        21        31        41        51        61        71        81        91       101 
            CVN_NOSEL     2 GKFSQTCYNSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKWQPSNFIETCRNTQLAGSSELAAECKTRAQQFVSTKINLDDHIANIDGTLKYE-   -
               SCOP domains d2rdka_ A: automated matches                                                                          SCOP domains
               CATH domains 2rdkA00 A:2-102 HIV-inactivating Protein,Cyanovirin-n;                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhheeeeeee..eeeeeee.....eeeeeee....eeee..eeee...hhhh.eeeeeee...eeeeeee.....eeeeeee....eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 2rdk A   2 GNFSQACYNSAIQGSVLTSTCIRTNGGYNTSSIDLNSVIENVDGSLKWQGSNFIETCRNTQLAGSSELAAECKTRAQQFVSTKINLDDHIAAIDGTLKYEL 102
                                    11        21        31        41        51        61        71        81        91       101 


Chain B from PDB  Type:PROTEIN  Length:99
 aligned with CVN_NOSEL | P81180 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:99
                                    12        22        32        42        52        62        72        82        92         
            CVN_NOSEL     3 KFSQTCYNSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKWQPSNFIETCRNTQLAGSSELAAECKTRAQQFVSTKINLDDHIANIDGTLKYE 101
               SCOP domains d2rdkb_ B: automated matches                                                                        SCOP domains
               CATH domains 2rdkB00 B:3-101 HIV-inactivating Protein,Cyanovirin-n;                                              CATH domains
           Pfam domains (1) CVNH-2rdkB01 B:3-100                                                                              - Pfam domains (1)
           Pfam domains (2) CVNH-2rdkB02 B:3-100                                                                              - Pfam domains (2)
         Sec.struct. author hhhh.eeeeeee..eeeeeee.....eeeeeee.hhh.eee..eee....hhhh.eeeeeee...eeeeeee.....eeeeeee....eeee..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 2rdk B   3 NFSQACYNSAIQGSVLTSTCIRTNGGYNTSSIDLNSVIENVDGSLKWQGSNFIETCRNTQLAGSSELAAECKTRAQQFVSTKINLDDHIAAIDGTLKYE 101
                                    12        22        32        42        52        62        72        82        92
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: CVNH] (11)

(-) Gene Ontology  (2, 2)

Asymmetric 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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 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 2rp3 2z21 3czz 3ezm 3gxy 3gxz 3lhc 3s3y 3s3z 4j4c 4j4d 4j4e 4j4f 4j4g

(-) Related Entries Specified in the PDB File

1iiy NMR WITH MANNOSE MONOMER
1lom DOMAIN -SWAP-DIMER
1m5m MAN-9 RES 2.5 A
2pys FIVE FOLD CYANOVIRIN-N MUTATION AT 1.8 A WITH MANNOSE
2z21 FIVE FOLD CYANOVIRIN-N MUTATION AT 1.8 A
3ezm WILD-TYPE 1.5 A WITHOUT LIGAND