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

(-) Description

Title :  GALECTIN DOMAIN OF PORCINE ADENOVIRUS TYPE 4 NADC-1 ISOLATE FIBRE COMPLEXED WITH N-ACETYL-LACTOSAMINE
 
Authors :  P. Guardado-Calvo, E. M. Munoz, A. L. Llamas-Saiz, G. C. Fox, J. N. Glasg M. J. Van Raaij
Date :  10 Sep 09  (Deposition) - 11 Aug 10  (Release) - 13 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym./Biol. Unit :  A
Keywords :  Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Guardado-Calvo, E. M. Munoz, A. L. Llamas-Saiz, G. C. Fox, R. Kahn, D. T. Curiel, J. N. Glasgow, M. J. Van Raaij
Crystallographic Structure Of Porcine Adenovirus 4 Fibre 2 Head And Galectin Domains.
J. Virol. V. 84 10558 2010
PubMed-ID: 20686025  |  Reference-DOI: 10.1128/JVI.00997-10
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE FIBER PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: GALECTIN DOMAIN, RESIDUES 393-703
    Organism Scientific: PORCINE ADENOVIRUS 4
    Organism Taxid: 35267
    Variant: NADC-1 ISOLATE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3NO34Ligand/IonNITRATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:415 , PRO A:416 , SER A:417 , ASP A:546 , ALA A:547 , TYR A:548 , VAL A:549 , HOH A:2067BINDING SITE FOR RESIDUE NO3 A1686
2AC2SOFTWAREILE A:392 , PRO A:393 , PHE A:394 , VAL A:395 , THR A:569 , PRO A:570 , LEU A:571BINDING SITE FOR RESIDUE NO3 A1687
3AC3SOFTWAREASN A:578 , VAL A:580 , HIS A:584 , SER A:587 , HIS A:670 , HOH A:2156BINDING SITE FOR RESIDUE NO3 A1688
4AC4SOFTWAREARG A:439 , PRO A:441 , HIS A:584 , TYR A:585 , HOH A:2015 , HOH A:2157 , HOH A:2158BINDING SITE FOR RESIDUE NO3 A1689
5AC5SOFTWAREHIS A:435 , ASN A:437 , ARG A:439 , ASN A:451 , GLU A:462 , TYR A:585 , ASP A:586 , NAG A:1691 , HOH A:2092 , HOH A:2159 , HOH A:2160BINDING SITE FOR RESIDUE GAL A1690
6AC6SOFTWAREARG A:439 , GLU A:462 , ARG A:464 , GLY A:617 , SER A:618 , GLU A:619 , GAL A:1690 , HOH A:2160 , HOH A:2161 , HOH A:2162 , HOH A:2163BINDING SITE FOR RESIDUE NAG A1691

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WT0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WT0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WT0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WT0)

(-) Exons   (0, 0)

(no "Exon" information available for 2WT0)

(-) 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:300
 aligned with Q83467_ADEP4 | Q83467 from UniProtKB/TrEMBL  Length:703

    Alignment length:334
                                   361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681    
         Q83467_ADEP4   352 EAEPPRKPPRGDLAALYNRVHSDTRAEDTPTSPELVTTLPDPFVLPLPDGVPTGASIVLEGTLTPSAVFFTLDLVTGPASLALHFNVRLPLEGEKHIVCNSREGSSNWGEEVRPQEFPFEREKPFVLVIVIQSDTYQITVNGKPLVDFPQRLQGITRASLSGDLVFTRLTMYPPGDPRPTTLLPPPAAPLDVIPDAYVLNLPTGLTPRTLLTVTGTPTPLAEFFIVNLVYDLHYDSKNVALHFNVGFTSDSKGHIACNARMNGTWGSEITVSDFPFQRGKPFTLQILTREADFQVLVDKQPLTQFQYRLKELDQIKYVHMFGHVVQTHLEHQVP 685
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Gal-bind_lectin-2wt0A01 A:547-682                                                                                                       --- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Gal-bind_lectin-2wt0A02 A:547-682                                                                                                       --- Pfam domains (2)
         Sec.struct. author ........----------------------------------.eee.........eeeeeeee.....eeeeeee.....eeeeeeee.......eeeeeee........................eeeee...eeeeee...eeeeee.......eeeee..eeeeeeeee.....hhhhh...............eee.........eeeeeeee......eeeeee.........eeeeeee.........eeeeee........eee............eeeee...eeeeee..eeeeeee....hhhhh.eeeee..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wt0 A 386 GGQQGRIP----------------------------------FVLPLPDGVPTGASIVLEGTLTPSAVFFTLDLVTGPASLALHFNVRLPLEGEKHIVCNSREGSSNWGEEVRPQEFPFEREKPFVLVIVIQSDTYQITVNGKPLVDFPQRLQGITRASLSGDLVFTRLTMYPPGDPRPTTLLPPPAAPLDVIPDAYVLNLPTGLTPRTLLTVTGTPTPLAEFFIVNLVYDLHYDSKNVALHFNVGFTSDSKGHIACNARMNGTWGSEITVSDFPFQRGKPFTLQILTREADFQVLVDKQPLTQFQYRLKELDQIKYVHMFGHVVQTHLEHQVP 685
                                   | -         -         -         -  |    401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681    
                                 393                                394
   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  (0, 0)

(no "SCOP Domain" information available for 2WT0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WT0)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Concanavalin (293)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q83467_ADEP4 | Q83467)
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:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0019058    viral life cycle    A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.

 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
    GAL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NO3  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2wt0)
 

(-) 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
  2wt0
    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
  Q83467_ADEP4 | Q83467
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q83467_ADEP4 | Q83467
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q83467_ADEP4 | Q83467: 2wst 2wsu 2wsv 2wt1 2wt2

(-) Related Entries Specified in the PDB File

2wst HEAD DOMAIN OF PORCINE ADENOVIRUS TYPE 4 NADC-1 ISOLATE FIBRE
2wsu GALECTIN DOMAIN OF PORCINE ADENOVIRUS TYPE 4 NADC-1 ISOLATE FIBRE
2wsv GALECTIN DOMAIN OF PORCINE ADENOVIRUS TYPE 4 NADC-1 ISOLATE FIBRE COMPLEXED WITH LACTOSE
2wt1 GALECTIN DOMAIN OF PORCINE ADENOVIRUS TYPE 4 NADC-1 ISOLATE FIBRE COMPLEXED WITH LACTO -N-NEO-TETRAOSE
2wt2 GALECTIN DOMAIN OF PORCINE ADENOVIRUS TYPE 4 NADC-1 ISOLATE FIBRE COMPLEXED WITH TRI( N-ACETYL-LACTOSAMINE)