Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) 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
    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, 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)
  - → 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  (1, 2)

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

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:83 - Pro A:84   [ RasMol ]  
    Gly B:83 - Pro B:84   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2hyq
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  GRFIN_GRISQ | P84801
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  GRFIN_GRISQ | P84801
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        GRFIN_GRISQ | P84801: 2gty 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