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

(-) Description

Title :  CRYSTAL STRUCTURE OF H1 HEMAGGLUTININ FROM A/WASHINGTON/05/2011 IN COMPLEX WITH A NEUTRALIZING ANTIBODY 3E1
 
Authors :  W. Wang, T. Zhang, J. Ding
Date :  01 Jul 16  (Deposition) - 07 Dec 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  A,B,H,L  (3x)
Keywords :  Epitope, Fab, Complementarity Determining Region, Paratope, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Wang, X. Sun, Y. Li, J. Su, Z. Ling, T. Zhang, F. Wang, H. Zhang, H. Chen J. Ding, B. Sun
Human Antibody 3E1 Targets The Ha Stem Region Of H1N1 And H5N6 Influenza A Viruses
Nat Commun V. 7 13577 2016
PubMed-ID: 27910950  |  Reference-DOI: 10.1038/NCOMMS13577

(-) Compounds

Molecule 1 - HEMAGGLUTININ
    Chains: A
    Engineered: YES
    Expression System: BACULOVIRUS EXPRESSION VECTOR PFASTBAC1-HM
    Expression System Plasmid: PFAST-HTB
    Expression System Strain: SF9
    Expression System Taxid: 274590
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1344
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 1318439
    Strain: A/WASHINGTON/05/2011(H1N1)
 
Molecule 2 - HEMAGGLUTININ
    Chains: B
    Engineered: YES
    Expression System: BACULOVIRUS EXPRESSION VECTOR PFASTBAC1-HM
    Expression System Plasmid: PFAST-HTB
    Expression System Strain: SF9
    Expression System Taxid: 274590
    Expression System Vector Type: PLASMID
    Fragment: HEMAGGLUTININ
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 1318439
    Strain: A/WASHINGTON/05/2011(H1N1)
 
Molecule 3 - LIGHT CHAIN OF HUMAN NEUTRALIZING ANTIBODY 3E1
    Chains: L
    Engineered: YES
    Expression System: CLONING VECTOR ABVEC-HIGKAPPA
    Expression System Plasmid: ABVEC-HIGKAPPA2
    Expression System Strain: HEK-293T
    Expression System Taxid: 583343
    Expression System Vector Type: PLASMID
    Fragment: LIGHT CHAIN OF NEUTRALIZING ANTIBODY 3E1
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - HEAVY CHAIN OF HUMAN NEUTRALIZING ANTIBODY 3E1
    Chains: H
    Engineered: YES
    Expression System: CLONING VECTOR ABVEC-HIGG1
    Expression System Plasmid: ABVEC-HIGG1
    Expression System Strain: HEK-293T
    Expression System Taxid: 583342
    Expression System Vector Type: PLASMID
    Fragment: HEAVY CHAIN OF NEUTRALIZING ANTIBODY 3E1
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABHL
Biological Unit 1 (3x): ABHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:74 , ASP A:96 , ASN A:97 , CYS A:100 , ARG A:231binding site for Poly-Saccharide residues NAG A 401 through NAG A 402 bound to ASN A 97

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:14 -B:137
2A:52 -A:285
3A:65 -A:77
4A:100 -A:146
5A:289 -A:313
6B:144 -B:148
7H:22 -H:95
8H:148 -H:204
9L:23 -L:88
10L:134 -L:194

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Thr A:298 -Ser A:299
2Ser L:7 -Pro L:8
3Tyr L:94 -Pro L:95
4Tyr L:140 -Pro L:141
5Ser L:182 -Lys L:183
6Ser H:54 -Gly H:55
7Gly H:104 -Gly H:105
8Phe H:154 -Pro H:155
9Glu H:156 -Pro H:157

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GJT)

(-) 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:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhhhhhhh..........eee...............hhhhhhhhhh.....eeee................................eee..........eeeeee.....eeeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeee.....eee....eeeeee.ee...........ee......eee..ee......eee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gjt A  10 SDTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKGFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTTADQQSLYQNADTYVFVGTSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVP 332
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269||     281       291       301       311       321       331 
                                                                                                                                                                                                                                                                                              270|                                                           
                                                                                                                                                                                                                                                                                               273                                                           


Chain B from PDB  Type:PROTEIN  Length:165
                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeee....eeeeehhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee..eeee....hhhhhhhhhh....hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gjt B   5 AIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDKITNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRNQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLN 169
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164     


Chain H from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee.....eeeeee......ee.......eeeeee....eeeeee...hhhhheeeeeeee.........eeee...eeeee........eeeee...eeeeeeeeee.....eeee........eee...ee.....eeeeeeeee.........eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gjt H   1 QVQLQESGPGLVKPSETLSLTCSVSGASISSYYWIWIRQPGKGLEWIGRFYTSGSPNYNPSLRSRVTMSVDTSKNQFSLKLTSVTAADTAVYYCAREEHITFGGVIVRYWGQGTLVTVSPASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGQTYICNVNHKPSNTKVDKKVEP 221
                                    10        20        30        40|       51        61        71        81        91       101       111       121       131  ||   149       159       169       179       189       200       210       220 
                                                                  40|                                                                                         134|                                                    198|                     
                                                                   42                                                                                          143                                                     200                     


Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee.....hhhhh...eeeeeeee.....eeeee.........eeeee.........eeeeeee..hhhhhhh.eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gjt L   1 DIQMTQSPATLSASVGDRVSITCRASQSISSWLAWYQQKPGKAPKLLIYKASSLESGVPSRFSGSGSGSEFTLTISSLQPDDFAIYYCQQYNSYPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180|      191       201       211 
                                                                                                                                                                                                             180|                              
                                                                                                                                                                                                              182
   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 5GJT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

 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
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu H:156 - Pro H:157   [ RasMol ]  
    Gly H:104 - Gly H:105   [ RasMol ]  
    Phe H:154 - Pro H:155   [ RasMol ]  
    Ser H:54 - Gly H:55   [ RasMol ]  
    Ser L:182 - Lys L:183   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Thr A:298 - Ser A:299   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
    Tyr L:94 - Pro L:95   [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  5gjt
    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
  N0C8E5_9INFA | N0C8E5
    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
  N0C8E5_9INFA | N0C8E5
    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 5GJT)

(-) Related Entries Specified in the PDB File

5gjs