Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  NANOPOROUS CRYSTALS OF CHICKEN EMBRYO LETHAL ORPHAN (CELO) ADENOVIRUS MAJOR COAT PROTEIN, HEXON
 
Authors :  L. Xu, S. D. Benson, R. M. Burnett
Date :  09 Oct 06  (Deposition) - 06 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Avian Adenovirus, Celo, Major Coat Protein, Hexon, Crystal Packing, Nanotechnology, Viral Jelly Roll, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Xu, S. D. Benson, R. M. Burnett
Nanoporous Crystals Of Chicken Embryo Lethal Orphan (Celo) Adenovirus Major Coat Protein, Hexon.
J. Struct. Biol. V. 157 424 2007
PubMed-ID: 17071105  |  Reference-DOI: 10.1016/J.JSB.2006.08.017
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEXON PROTEIN
    Chains: A
    Organism Scientific: FOWL ADENOVIRUS 1
    Organism Taxid: 10553
    Strain: PHELPS STRAIN
    Synonym: LATE PROTEIN 2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2INY)

(-) Sites  (0, 0)

(no "Site" information available for 2INY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Trp A:700 -Pro A:701
2Trp A:833 -Pro A:834
3Thr A:933 -Pro A:934

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2INY)

(-) 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:941
 aligned with CAPSH_ADEG1 | P42671 from UniProtKB/Swiss-Prot  Length:942

    Alignment length:941
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       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       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941 
          CAPSH_ADEG1     2 TALTPDLTTATPRLQYFHIAGPGTREYLSEDLQQFISATGSYFDLKNKFRQTVVAPTRNVTTEKAQRLQIRFYPIQTDDTPNSYRVRYSVNVGDSWVLDMGATYFDIKGVLDRGPSFKPYGGTAYNPLAPREAIFNTWVESTGPQTNVVGQMTNVYTNQTRNDKTATLQQVNSISGVVPNVNLGPGLSQLASRADVDNIGVVGRFAKVDSAGVKQAYGAYVKPVKDDGSQSLNQTAYWLMDNGGTNYLGALAVEDYTQTLSYPDTVLVTPPTAYQQVNSGTMRACRPNYIGFRDNFINLLYHDSGVCSGTLNSERSGMNVVVELQDRNTELSYQYMLADMMSRHHYFALWNQAVDQYDHDVRVFNNDGYEEGVPTYAFLPDGHGAGEDNGPDLSNVKIYTNGQQDKGNVVAGTVSTQLNFGTIPSYEIDIAAATRRNFIMSNIADYLPDKYKFSIRGFDPVTDNIDPTTYFYMNRRVPLTNVVDLFTNIGARWSVDQMDNVNPFNHHRNWGLKYRSQLLGNSRYCRFHIQVPQKYFAIKNLLLLPGTYTYEWVLRKDPNMILQSSLGNDLRADGAQIVYTEVNLMANFMPMDHNTSNQLELMLRNATNDQTFADYLGAKNALYNVPAGSTLLTINIPARTWEGMRGWSFTRLKASETPQLGAQYDVGFKYSGSIPYSDGTFYLSHTFRSMSVLFDTSINWPGNDRLLTPNLFEIKRPVATDSEGFTMSQCDMTKDWFLVQMATNYNYVYNGYRFWPDRHYFHYDFLRNFDPMSRQGPNFLDTTLYDLVSSTPVVNDTGSQPSQDNVRNNSGFIAPRSWPVWTAQQGEAWPANWPYPLIGNDAISSNQTVNYKKFLCDNYLWTVPFSSDFMYMGELTDLGQNPMYTNNSHSMVINFELDPMDENTYVYMLYGVFDTVRVNQPERNVLAMAYFRTPFATGNAV 942
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhh...........hhhhhhhhhhh.............................eeee..........eeeeee................eee................................................................................................eee...........................eeeee............eeeeee.................................ee.hhhhh......hhhhh....................hhhhhhhhhhhhh................hhhhhh................................ee..........ee...................hhhhhhhhhhhhhhhhhhhhhhhhee..............hhhhhh.ee.hhhhh...........hhhhh.........hhhhhhhh............eee..................eeeeee.......ee..................eeeee....hhhhhhhhhhhhh.............eeee.........eeeeeeeee......eeee........................hhhhh..........eeeeee...ee............ee..........................................hhhhh........eee..................................................................................eee.....eee........................eeeeeeee...........eeee.............................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iny A   1 TALTPDLTTATPRLQYFHIAGPGTREYLSEDLQQFISATGSYFDLKNKFRQTVVAPTRNVTTEKAQRLQIRFYPIQTDDTPNSYRVRYSVNVGDSWVLDMGATYFDIKGVLDRGPSFKPYGGTAYNPLAPREAIFNTWVESTGPQTNVVGQMTNVYTNQTRNDKTATLQQVNSISGVVPNVNLGPGLSQLASRADVDNIGVVGRFAKVDSAGVKQAYGAYVKPVKDDGSQSLNQTAYWLMDNGGTNYLGALAVEDYTQTLSYPDTVLVTPPTAYQQVNSGTMRACRPNYIGFRDNFINLLYHDSGVCSGTLNSERSGMNVVVELQDRNTELSYQYMLADMMSRHHYFALWNQAVDQYDHDVRVFNNDGYEEGVPTYAFLPDGHGAGEDNGPDLSNVKIYTNGQQDKGNVVAGTVSTQLNFGTIPSYEIDIAAATRRNFIMSNIADYLPDKYKFSIRGFDPVTDNIDPTTYFYMNRRVPLTNVVDLFTNIGARWSVDQMDNVNPFNHHRNWGLKYRSQLLGNSRYCRFHIQVPQKYFAIKNLLLLPGTYTYEWVLRKDPNMILQSSLGNDLRADGAQIVYTEVNLMANFMPMDHNTSNQLELMLRNATNDQTFADYLGAKNALYNVPAGSTLLTINIPARTWEGMRGWSFTRLKASETPQLGAQYDVGFKYSGSIPYSDGTFYLSHTFRSMSVLFDTSINWPGNDRLLTPNLFEIKRPVATDSEGFTMSQCDMTKDWFLVQMATNYNYVYNGYRFWPDRHYFHYDFLRNFDPMSRQGPNFLDTTLYDLVSSTPVVNDTGSQPSQDNVRNNSGFIAPRSWPVWTAQQGEAWPANWPYPLIGNDAISSNQTVNYKKFLCDNYLWTVPFSSDFMYMGELTDLGQNPMYTNNSHSMVINFELDPMDENTYVYMLYGVFDTVRVNQPERNVLAMAYFRTPFATGNAV 941
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940
   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 2INY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (CAPSH_ADEG1 | P42671)
molecular function
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0075521    microtubule-dependent intracellular transport of viral material towards nucleus    The directed movement of a virus, or part of a virus, towards the host cell nucleus using host microtubules.
    GO:0075606    transport of viral material towards nucleus    The directed movement of a virus, or part of a virus, towards the host cell nucleus. The process begins after viral entry, and ends when the viral material is at the nuclear membrane.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0039623    T=25 icosahedral viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=25 symmetry. The T=25 capsid is composed of 12 pentameric and 240 hexameric capsomeres.
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

 Visualization

(-) Interactive Views

Asymmetric 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
(no "Ligands, Modified Residues, Ions" information available for 2iny)
 
  Sites
(no "Sites" information available for 2iny)
 
  Cis Peptide Bonds
    Thr A:933 - Pro A:934   [ RasMol ]  
    Trp A:700 - Pro A:701   [ RasMol ]  
    Trp A:833 - Pro A:834   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 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
  2iny
    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
  CAPSH_ADEG1 | P42671
    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
  CAPSH_ADEG1 | P42671
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2INY)

(-) Related Entries Specified in the PDB File

1hx6 MAJOR COAT PROTEIN OF BACTERIOPHAGE PRD1
1m3y MAJOR COAT PROTEIN OF PBCV-1
1p2z HUMAN ADENOVIRUS TYPE 2 HEXON
1p30 HUMAN ADENOVIRUS TYPE 5 HEXON
2bbd MAJOR COAT PROTEIN OF STIV