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(-) Description

Title :  GALECTIN DOMAIN OF PORCINE ADENOVIRUS TYPE 4 NADC-1 ISOLATE FIBRE COMPLEXED WITH TRI(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 :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
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, B
    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

  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  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1GAL6Ligand/IonBETA-D-GALACTOSE
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
3NO36Ligand/IonNITRATE ION
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1GAL3Ligand/IonBETA-D-GALACTOSE
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
3NO33Ligand/IonNITRATE ION
Biological Unit 2 (3, 9)
No.NameCountTypeFull Name
1GAL3Ligand/IonBETA-D-GALACTOSE
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
3NO33Ligand/IonNITRATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:393 , PHE A:394 , VAL A:395 , THR A:569 , PRO A:570 , LEU A:571BINDING SITE FOR RESIDUE NO3 A1686
02AC2SOFTWARETHR A:415 , PRO A:416 , SER A:417 , ASP A:546 , ALA A:547 , TYR A:548 , VAL A:549 , HOH A:2059BINDING SITE FOR RESIDUE NO3 A1687
03AC3SOFTWAREASN A:578 , VAL A:580 , HIS A:584 , SER A:587 , HIS A:670BINDING SITE FOR RESIDUE NO3 A1688
04AC4SOFTWAREPRO B:393 , PHE B:394 , VAL B:395 , THR B:569 , PRO B:570 , LEU B:571BINDING SITE FOR RESIDUE NO3 B1686
05AC5SOFTWARETHR B:415 , PRO B:416 , SER B:417 , ASP B:546 , ALA B:547 , TYR B:548 , VAL B:549 , HOH B:2031BINDING SITE FOR RESIDUE NO3 B1687
06AC6SOFTWAREASN B:578 , VAL B:580 , HIS B:584 , SER B:587 , HIS B:670BINDING SITE FOR RESIDUE NO3 B1688
07AC7SOFTWARELYS B:446 , GLU B:471 , ALA B:572 , GLU B:573 , PHE B:598 , ARG B:629 , NAG B:1690BINDING SITE FOR RESIDUE GAL B1689
08AC8SOFTWAREALA B:430 , LEU B:432 , ARG B:453 , GLU B:573 , PHE B:598 , GAL B:1689 , GAL B:1691BINDING SITE FOR RESIDUE NAG B1690
09AC9SOFTWAREARG B:453 , PHE B:574 , ILE B:576 , NAG B:1690 , NAG B:1692 , HOH B:2068BINDING SITE FOR RESIDUE GAL B1691
10BC1SOFTWAREASP B:424 , LEU B:432 , HIS B:435 , ARG B:453 , TRP B:459 , TYR B:585 , GAL B:1691 , GAL B:1693 , HOH B:2007 , HOH B:2042BINDING SITE FOR RESIDUE NAG B1692
11BC2SOFTWAREHIS B:435 , ASN B:437 , ARG B:439 , VAL B:449 , ASN B:451 , TRP B:459 , GLU B:462 , TYR B:585 , NAG B:1692 , NAG B:1694BINDING SITE FOR RESIDUE GAL B1693
12BC3SOFTWARELYS A:650 , ARG B:439 , GLU B:462 , ARG B:464 , GAL B:1693BINDING SITE FOR RESIDUE NAG B1694
13BC4SOFTWARELYS A:446 , GLU A:471 , GLU A:573 , PHE A:598 , ARG A:629 , NAG A:1690BINDING SITE FOR RESIDUE GAL A1689
14BC5SOFTWAREALA A:430 , LEU A:432 , ARG A:453 , GLU A:573 , GAL A:1689 , GAL A:1691BINDING SITE FOR RESIDUE NAG A1690
15BC6SOFTWAREARG A:453 , PHE A:574 , NAG A:1690 , NAG A:1692 , HOH A:2005BINDING SITE FOR RESIDUE GAL A1691
16BC7SOFTWAREASP A:424 , LEU A:432 , HIS A:435 , ARG A:453 , TRP A:459 , TYR A:585 , GAL A:1691 , GAL A:1693BINDING SITE FOR RESIDUE NAG A1692
17BC8SOFTWAREHIS A:435 , ASN A:437 , ARG A:439 , VAL A:449 , ASN A:451 , TRP A:459 , GLU A:462 , TYR A:585 , NAG A:1692 , NAG A:1694BINDING SITE FOR RESIDUE GAL A1693
18BC9SOFTWAREARG A:439 , GLU A:462 , ARG A:464 , GAL A:1693 , HOH A:2061BINDING SITE FOR RESIDUE NAG A1694

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WT2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WT2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WT2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WT2)

(-) Exons   (0, 0)

(no "Exon" information available for 2WT2)

(-) 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: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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........----------------------------------.eee.........eeeeeeee.....eeeeeeee...eeeeeeeee.......eeeeeee........................eeeee...eeeeee...eeeeee.......eeeee..eeeeeeeee.........................eee.........eeeeeeee......eeeeee.........eeeeeee.........eeeeee........eee............eeeee...eeeeee..eeeeeee....hhhhh.eeeee..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wt2 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                                                                                                                                                                                                                                                                                                   


Chain B 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-2wt2B01 B:547-682                                                                                                       --- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Gal-bind_lectin-2wt2B02 B:547-682                                                                                                       --- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Gal-bind_lectin-2wt2B03 B:547-682                                                                                                       --- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Gal-bind_lectin-2wt2B04 B:547-682                                                                                                       --- Pfam domains (4)
         Sec.struct. author ........----------------------------------.eee.........eeeeeeee.....eeeeeeee...eeeeeeeee.......eeeeeee........................eeeee...eeeeee...eeeeee.......eeeee..eeeeeeeee.........................eee.........eeeeeeee......eeeeee.........eeeeeee.........eeeeee........eee............eeeee...eeeeee..eeeeeee....hhhhh.eeeee..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wt2 B 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 2WT2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WT2)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Concanavalin (293)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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.

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  2wt2
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 Related Entries

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

UniProtKB/TrEMBL
        Q83467_ADEP4 | Q83467: 2wst 2wsu 2wsv 2wt0 2wt1

(-) 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
2wt0 GALECTIN DOMAIN OF PORCINE ADENOVIRUS TYPE 4 NADC-1 ISOLATE FIBRE COMPLEXED WITH N- ACETYL-LACTOSAMINE
2wt1 GALECTIN DOMAIN OF PORCINE ADENOVIRUS TYPE 4 NADC-1 ISOLATE FIBRE COMPLEXED WITH LACTO -N-NEO-TETRAOSE