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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  A VIRAL CAPSID:ANTIBODY COMPLEX
 
Authors :  L. James
Date :  27 Jun 16  (Deposition) - 12 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Trim21, 9C12, Adenovirus, Neutralization, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. James
Structure Of A Virus Capsid:Antibody Complex
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HEXON PROTEIN,HEXON CAPSID
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: L3
    Organism Common: HADV-5
    Organism Scientific: HUMAN ADENOVIRUS C SEROTYPE 5, HUMAN ADENOVIRUS 5
    Organism Taxid: 28285
    Synonym: CP-H,PROTEIN II
 
Molecule 2 - ANTIBODY
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - ANTIBODY
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5LDN)

(-) Sites  (0, 0)

(no "Site" information available for 5LDN)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:413 -A:413
2H:21 -H:94
3H:143 -H:198
4L:43 -L:108
5L:154 -L:214

(-) Cis Peptide Bonds  (17, 17)

Asymmetric/Biological Unit
No.Residues
1Ala A:137 -Ala A:138
2Ile A:143 -Asn A:144
3Gln A:200 -Pro A:201
4Lys A:256 -Leu A:257
5Leu A:257 -Glu A:258
6Gly A:274 -Asn A:275
7Trp A:730 -Pro A:731
8Phe A:845 -Pro A:846
9Thr A:942 -Pro A:943
10Thr L:27 -Pro L:28
11Ser L:114 -Pro L:115
12Tyr L:160 -Pro L:161
13Gly H:7 -Pro H:8
14Ser H:99 -Asn H:100
15Phe H:149 -Pro H:150
16Glu H:151 -Pro H:152
17Trp H:191 -Pro H:192

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LDN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LDN)

(-) Exons   (0, 0)

(no "Exon" information available for 5LDN)

(-) 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:927
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhh....hhhhh...................eeee...eeee...eeeeeeeeee.....ee.hhheeeeeeeee........................eeeee..............eeeee....ee...ee..eeeee......ee.......................eeeeee............ee........................eeeee................eeeeee...ee...eeeee.........hhhhhheeee.....eee.hhhh......hhhhh.eeee..............hhhhhhhhhhhhhh.....hhhhh......hhhhhhee.........eee.........eee..eee.......eee........eee.......eeehhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhh..hhhhhh.......ee.hhhhhh........hhhhhhhhhhhh...eeeeeeee..........ee..eeeeeeeeee.hhhhheee...........eeeeeeeeeeee....hhhhhhhhhhhhhhhhhheeee....eeeeeeee.....eeeeeeeee......eeeeeeee.hhh................hhhhhh...hhh.eeeeeeee...eee...........ee.................hhhhhhhhhhhhhh.........hhhhh...hhhhheeeeeeeee...................................................eeeeeeeee....eeee................hhhhhh..eeeeeeeee......eeeeeeee.eeeeeee.......eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ldn A   7 PQWSYMHISGQDASEYLSPGLVQFARATETYFSLNNKFRNPTVAPTHDVTTDRSQRLTLRFIPVDREDTAYSYKARFTLAVGDNRVLDMASTYFDIRGVLDRGPTFKPYSGTAYNALAPKGAPNPCEWDEAATALEINLAQAEQKTHVFGQAPYSGINITKEGIQIGVEGQTPKYADKTFQPEPQIGESQWYETEINHAAGRVLKKTTPMKPCYGSYAKPTNENGGQGILVKQQNGKLESQVEMQFFSTTEATAGNGDNLTPKVVLYSEDVDIETPDTHISYMPTIKEGNSRELMGQQSMPNRPNYIAFRDNFIGLMYYNSTGNMGVLAGQASQLNAVVDLQDRNTELSYQLLLDSIGDRTRYFSMWNQAVDSYDPDVRIIENHGTEDELPNYCFPLGGVINTETLTKVKPKTGQENGWEKDATEFSDKNEIRVGNNFAMEINLNANLWRNFLYSNIALYLPDKLKYSPSNVKISDNPNTYDYMNKRVVAPGLVDCYINLGARWSLDYMDNVNPFNHHRNAGLRYRSMLLGNGRYVPFHIQVPQKFFAIKNLLLLPGSYTYEWNFRKDVNMVLQSSLGNDLRVDGASIKFDSICLYATFFPMAHNTASTLEAMLRNDTNDQSFNDYLSAANMLYPIPANATNVPISIPSRNWAAFRGWAFTRLKTKETPSLGSGYDPYYTYSGSIPYLDGTFYLNHTFKKVAITFDSSVSWPGNDRLLTPNEFEIKRSVDGEGYNVAQCNMTKDWFLVQMLANYNIGYQGFYIPESYKDRMYSFFRNFQPMSRQVVDDTKYKDYQQVGILHQHNNSGFVGYLAPTMREGQAYPANFPYPLIGKTAVDSITQKKFLCDRTLWRIPFSSNFMSMGALTDLGQNLLYANSAHALDMTFEVDPMDEPTLLYVLFEVFDVVRVHRPHRGVIETVYLRTPFSA 946
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       
                                                                                                                                                                    145|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
                                                                                                                                                                     159                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   


Chain H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....ee........eeee.........eeeeee.....eeeeeee......ee.hhhhh.eeeeee....eeeeee........eeeeeeee.....eeee....eeee........eeeee..........eeeeeeeeeee.....eeee........eee...ee....eee.eeeeee..........eeee........ee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ldn H   1 VQLKQSGPGLLQPSQRLSITCTVSGFSLGRYGVHWIRQSPGKGLEWLGVIWRGGTTDYNAVFMSRLSINKDDSKSQVFFTMNSLRPDDTAIYYCARQGSNFPLAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPRDC 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..ee.......eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eee.........eeee...........eeeeeeeee..........ee..........................eeeeeee........eeee..............ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ldn L  21 NIVMTQTPKFLLVSIGDSITITCKASQSVTNDAAWYQKKPGQSPQLLIYQASTRYTGVPDRFSGSGYGTDFTFTISAVQAEDLAVYFCHQDYSSPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 233
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
   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 5LDN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LDN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LDN)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5LDN)

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Asymmetric/Biological Unit
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  Ligands, Modified Residues, Ions
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  Sites
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  Cis Peptide Bonds
    Ala A:137 - Ala A:138   [ RasMol ]  
    Gln A:200 - Pro A:201   [ RasMol ]  
    Glu H:151 - Pro H:152   [ RasMol ]  
    Gly A:274 - Asn A:275   [ RasMol ]  
    Gly H:7 - Pro H:8   [ RasMol ]  
    Ile A:143 - Asn A:144   [ RasMol ]  
    Leu A:257 - Glu A:258   [ RasMol ]  
    Lys A:256 - Leu A:257   [ RasMol ]  
    Phe A:845 - Pro A:846   [ RasMol ]  
    Phe H:149 - Pro H:150   [ RasMol ]  
    Ser H:99 - Asn H:100   [ RasMol ]  
    Ser L:114 - Pro L:115   [ RasMol ]  
    Thr A:942 - Pro A:943   [ RasMol ]  
    Thr L:27 - Pro L:28   [ RasMol ]  
    Trp A:730 - Pro A:731   [ RasMol ]  
    Trp H:191 - Pro H:192   [ RasMol ]  
    Tyr L:160 - Pro L:161   [ RasMol ]  
 

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  CAPSH_ADE05 | P04133
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        CAPSH_ADE05 | P04133: 1p30 3iyn 3tg7 4cwu 4v4u

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