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(-) Description

Title :  CRYSTAL STRUCTURE OF UNLIGANDED GRIFFITHSIN
 
Authors :  N. E. Ziolkowska, A. Wlodawer
Date :  28 Apr 06  (Deposition) - 01 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
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, B. R. O'Keefe, T. Mori, C. Zhu, B. Giomarelli, F. Vojdani, K. E. Palmer, J. B. Mcmahon, A. Wlodawer
Domain-Swapped Structure Of The Potent Antiviral Protein Griffithsin And Its Mode Of Carbohydrate Binding.
Structure V. 14 1127 2006
PubMed-ID: 16843894  |  Reference-DOI: 10.1016/J.STR.2006.05.017
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GRIFFITHSIN
    Chains: A, B
    Engineered: YES
    Expression System: NICOTIANA BENTHAMIANA
    Expression System Taxid: 4100
    Organism Scientific: GRIFFITHSIA
    Organism Taxid: 35158
    Synonym: GRFT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric/Biological Unit (3, 16)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2EDO6Ligand/Ion1,2-ETHANEDIOL
3SO48Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:12 , TYR B:68 , GLY B:108 , ASP B:109 , TYR B:110 , ASP B:112BINDING SITE FOR RESIDUE SO4 B 301
02AC2SOFTWARETYR A:68 , GLY A:108 , ASP A:109 , TYR A:110 , ASP A:112 , HOH A:433 , GLY B:12BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWARESER A:27 , GLY A:87 , SER A:88 , TYR B:121 , HOH B:339BINDING SITE FOR RESIDUE SO4 B 303
04AC4SOFTWAREHIS A:4 , LYS A:6 , HOH A:369 , HOH A:397 , HOH A:420 , ARG B:80BINDING SITE FOR RESIDUE SO4 A 304
05AC5SOFTWAREGLY B:26 , SER B:27 , TYR B:28 , ASP B:30 , HOH B:423 , HOH B:429BINDING SITE FOR RESIDUE SO4 B 305
06AC6SOFTWAREHOH A:325 , HOH A:393 , ARG B:24 , ASN B:45 , LEU B:46 , HOH B:385 , HOH B:409 , HOH B:419BINDING SITE FOR RESIDUE SO4 B 306
07AC7SOFTWAREGLY B:66 , ASP B:67 , TYR B:68 , ASP B:70 , HOH B:396 , HOH B:437BINDING SITE FOR RESIDUE SO4 B 307
08AC8SOFTWAREASN A:104 , ASP A:115 , TYR A:117 , HOH A:377 , LYS B:6 , LYS B:99 , HOH B:339BINDING SITE FOR RESIDUE SO4 A 308
09AC9SOFTWAREGLY A:26 , SER A:27 , TYR A:28 , ASP A:30 , GLY A:44 , HOH A:413BINDING SITE FOR RESIDUE EDO A 311
10BC1SOFTWAREASN A:60 , MET A:61 , THR A:62 , SER A:73 , PHE A:74 , HOH A:443 , HOH A:446BINDING SITE FOR RESIDUE EDO A 312
11BC2SOFTWARESER A:16 , LEU A:18 , PHE A:52 , GLU A:56 , TYR A:57 , ILE A:58 , VAL A:100 , HOH A:374BINDING SITE FOR RESIDUE EDO A 313
12BC3SOFTWARETYR A:57 , HOH A:366BINDING SITE FOR RESIDUE EDO A 314
13BC4SOFTWARESER B:73 , PHE B:74 , ARG B:81 , PHE B:82 , GLY B:83 , SER B:91 , HOH B:343BINDING SITE FOR RESIDUE EDO B 315
14BC5SOFTWAREGLY A:17 , LEU A:18 , ASP A:35 , GLN A:102 , GLY B:17 , LEU B:18 , ASP B:35 , GLN B:102BINDING SITE FOR RESIDUE EDO A 316

(-) SS Bonds  (0, 0)

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

(-) 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 2GTY)

(-) 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 2GTY)

(-) 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 -d2gtya1 A: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: A:1-120 UniProt: 1-120                                                                             - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gty 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 -d2gtyb1 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
                 2gty B   0 xSLTHRKFGGSGGSPFSGLSSIAVRSGSYLDAIIIDGVHHGGSGGNLSPTFTFGSGEYISNMTIRSGDYIDNISFETNMGRRFGPYGGSGGSANTLSNVKVIQINGSAGDYLDSLDIYYEQY 121
                            |        9        19        29        39        49        59        69        79        89        99       109       119  
                            0-ACE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 | P84801: 2guc 2gud 2gue 2gux 2hyq 2hyr 2nu5 2nuo 3lky 3ll0 3ll1 3ll2

(-) Related Entries Specified in the PDB File

2guc 2gud 2gue 2gux