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(-) Description

Title :  CRYSTAL STRUCTURE OF A COMPLEX OF GRIFFITHSIN WITH 6ALPHA-MANNOBIOSE
 
Authors :  N. E. Ziolkowska, A. Wlodawer
Date :  07 Aug 06  (Deposition) - 24 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Griffithsin, Lectins, Domain Swapping, Mannose Binding, Hiv, Sars, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. E. Ziolkowska, S. R. Shenoy, B. R. O'Keefe, J. B. Mcmahon, K. E. Palmer, R. A. Dwek, M. R. Wormald, A. Wlodawer
Crystallographic, Thermodynamic, And Molecular Modeling Studies Of The Mode Of Binding Of Oligosaccharides To The Potent Antiviral Protein Griffithsin.
Proteins V. 67 661 2007
PubMed-ID: 17340634  |  Reference-DOI: 10.1002/PROT.21336

(-) Compounds

Molecule 1 - GRIFFITHSIN
    ChainsA, B
    EngineeredYES
    Expression SystemNICOTIANA BENTHAMIANA
    Expression System Taxid4100
    Organism ScientificGRIFFITHSIA
    Organism Taxid35158
    SynonymGRFT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric/Biological Unit (3, 17)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2MAN12Ligand/IonALPHA-D-MANNOSE
3SO43Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMAN A:123 , HOH A:252 , SO4 B:202BINDING SITE FOR RESIDUE MAN A 122
02AC2SOFTWAREGLY A:108 , ASP A:109 , TYR A:110 , ASP A:112 , MAN A:122 , GLY B:11 , GLY B:12 , GLN B:120BINDING SITE FOR RESIDUE MAN A 123
03AC3SOFTWARESER A:27 , MAN A:125BINDING SITE FOR RESIDUE MAN A 124
04AC4SOFTWAREGLY A:26 , SER A:27 , TYR A:28 , ASP A:30 , GLY A:44 , MAN A:124BINDING SITE FOR RESIDUE MAN A 125
05AC5SOFTWAREASP A:67 , MAN A:127BINDING SITE FOR RESIDUE MAN A 126
06AC6SOFTWAREGLY A:66 , ASP A:67 , TYR A:68 , ASP A:70 , GLY A:89 , GLY A:90 , MAN A:126BINDING SITE FOR RESIDUE MAN A 127
07AC7SOFTWARETYR B:28 , ASP B:67 , MAN B:123BINDING SITE FOR RESIDUE MAN B 122
08AC8SOFTWAREGLY B:66 , ASP B:67 , TYR B:68 , ASP B:70 , GLY B:89 , GLY B:90 , MAN B:122 , HOH B:239BINDING SITE FOR RESIDUE MAN B 123
09AC9SOFTWARESER B:27 , ARG B:64 , SER B:88 , MAN B:125 , SO4 B:203BINDING SITE FOR RESIDUE MAN B 124
10BC1SOFTWAREGLY B:26 , SER B:27 , TYR B:28 , ASP B:30 , GLY B:44 , MAN B:124BINDING SITE FOR RESIDUE MAN B 125
11BC2SOFTWAREMAN B:127BINDING SITE FOR RESIDUE MAN B 126
12BC3SOFTWAREGLY A:11 , GLY A:12 , ASN A:45 , TYR B:68 , GLY B:108 , ASP B:109 , TYR B:110 , ASP B:112 , MAN B:126 , HOH B:220 , HOH B:235BINDING SITE FOR RESIDUE MAN B 127
13BC4SOFTWAREARG A:64 , ALA A:92BINDING SITE FOR RESIDUE SO4 A 201
14BC5SOFTWAREARG A:5 , MAN A:122 , ASN B:93 , THR B:94BINDING SITE FOR RESIDUE SO4 B 202
15BC6SOFTWAREARG B:64 , GLY B:90 , ALA B:92 , MAN B:124BINDING SITE FOR RESIDUE SO4 B 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HYQ)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:83 -Pro A:84
2Gly B:83 -Pro B:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JACALIN_LECTINPS51752 Jacalin-type lectin domain profile.GRFIN_GRISQ1-120
 
  2A:1-120
B:1-120

(-) Exons   (0, 0)

(no "Exon" information available for 2HYQ)

(-) 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:122
 aligned with GRFIN_GRISQ | P84801 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:122
                             1                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119  
          GRFIN_GRISQ     - -SLTHRKFGGSGGSPFSGLSSIAVRSGSYLDXIIIDGVHHGGSGGNLSPTFTFGSGEYISNMTIRSGDYIDNISFETNMGRRFGPYGGSGGSANTLSNVKVIQINGSAGDYLDSLDIYYEQY 121
               SCOP domains -d2hyqa1 A:1-121 Griffithsin                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eee....eeeeee...eeeeee..eeee....ee...ee......eeeeeeee...eeeeeeee....eeeeee....eeeeee.eeeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -JACALIN_LECTIN  PDB: A:1-120 UniProt: 1-120                                                                             - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hyq A   0 xSLTHRKFGGSGGSPFSGLSSIAVRSGSYLDAIIIDGVHHGGSGGNLSPTFTFGSGEYISNMTIRSGDYIDNISFETNMGRRFGPYGGSGGSANTLSNVKVIQINGSAGDYLDSLDIYYEQY 121
                            |        9        19        29        39        49        59        69        79        89        99       109       119  
                            |                                                                                                                         
                            0-ACE                                                                                                                     

Chain B from PDB  Type:PROTEIN  Length:122
 aligned with GRFIN_GRISQ | P84801 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:122
                             1                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119  
          GRFIN_GRISQ     - -SLTHRKFGGSGGSPFSGLSSIAVRSGSYLDXIIIDGVHHGGSGGNLSPTFTFGSGEYISNMTIRSGDYIDNISFETNMGRRFGPYGGSGGSANTLSNVKVIQINGSAGDYLDSLDIYYEQY 121
               SCOP domains -d2hyqb1 B:1-121 Griffithsin                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eee....eeeeee...eeeeee..eeee....ee...ee......eeeeeeee...eeeeeeee....eeeeee....eeeeee.eeeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -JACALIN_LECTIN  PDB: B:1-120 UniProt: 1-120                                                                             - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hyq B   0 xSLTHRKFGGSGGSPFSGLSSIAVRSGSYLDAIIIDGVHHGGSGGNLSPTFTFGSGEYISNMTIRSGDYIDNISFETNMGRRFGPYGGSGGSANTLSNVKVIQINGSAGDYLDSLDIYYEQY 121
                            |        9        19        29        39        49        59        69        79        89        99       109       119  
                            0-ACE                                                                                                                     

   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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2HYQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HYQ)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GRFIN_GRISQ | P84801)
molecular function
    GO:0046871    N-acetylgalactosamine binding    Interacting selectively and non-covalently with N-acetylgalactosamine, 2-acetamido-2-deoxygalactopyranose, the n-acetyl derivative of galactosamine.
    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.
    GO:0005536    glucose binding    Interacting selectively and non-covalently with the D- or L-enantiomer of glucose.
    GO:0005537    mannose binding    Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GRFIN_GRISQ | P848012gty 2guc 2gud 2gue 2gux 2hyr 2nu5 2nuo 3lky 3ll0 3ll1 3ll2

(-) Related Entries Specified in the PDB File

2gty CRYSTAL STRUCTURE OF UNLIGANDED GRIFFITHSIN
2guc CRYSTAL STRUCTURE OF A COMPLEX OF GRIFFITHSIN WITH MANNOSE AT 1.78 A RESOLUTION
2gud CRYSTAL STRUCTURE OF A COMPLEX OF GRIFFITHSIN WITH MANNOSE AT 0.94 A RESOLUTION
2gue CRYSTAL STRUCTURE OF A COMPLEX OF GRIFFITHSIN WITH N- ACETYLGLUCOSAMINE
2gux SELENOMETHIONINE DERIVATIVE OF GRIFFITHSIN
2hyr CRYSTAL STRUCTURE OF A COMPLEX OF GRIFFITHSIN WITH MALTOSE