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 :  FAB STRUCTURE OF LIPID A-SPECIFIC ANTIBODY A6 IN COMPLEX WITH LIPID A CARBOHYDRATE BACKBONE
 
Authors :  O. Haji-Ghassemi, S. V. Evans
Date :  10 Jan 14  (Deposition) - 24 Jun 15  (Release) - 07 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Carbohydrate Binding, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Haji-Ghassemi, S. Muller-Loennies, T. Rodriguez, L. Brade, P. Kosma, H. Brade, S. V. Evans
Structural Basis For Antibody Recognition Of Lipid A: Insights To Polyspecificity Toward Single-Stranded Dna.
J. Biol. Chem. V. 290 19629 2015
PubMed-ID: 26085093  |  Reference-DOI: 10.1074/JBC.M115.657874

(-) Compounds

Molecule 1 - A6 FAB (IGG2B KAPPA) LIGHT CHAIN
    Chains: L
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 2 - A6 FAB (IGG2B) HEAVY CHAIN
    Chains: H
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1GP11Ligand/IonGLUCOSAMINE 1-PHOSPHATE
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3Z9M1Ligand/Ion2-AMINO-2-DEOXY-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN H:98 , ARG H:100A , CYS H:128 , GLY H:129 , ASP H:130 , THR H:132 , SER L:14 , ARG L:30 , TYR L:32 , TYR L:50 , Z9M L:302 , HOH L:405BINDING SITE FOR RESIDUE GP1 L 301
2AC2SOFTWARETYR H:96 , ASN H:98 , HIS H:100C , TYR L:49 , TYR L:50 , LYS L:53 , GP1 L:301BINDING SITE FOR RESIDUE Z9M L 302
3AC3SOFTWARETYR H:96 , ASP H:101 , TYR L:49 , HIS L:55BINDING SITE FOR RESIDUE PEG H 301

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:140 -H:195
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Leu L:94 -Pro L:95
2Tyr L:140 -Pro L:141
3Glu H:1 -Val H:2
4Lys H:64 -Gly H:65
5Cys H:128 -Gly H:129
6Asp H:130 -Thr H:131
7Phe H:146 -Pro H:147
8Glu H:148 -Ser H:149
9Ser H:156 -Gly H:157
10Trp H:188 -Pro H:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ODV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ODV)

(-) Exons   (0, 0)

(no "Exon" information available for 4ODV)

(-) 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 H from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeee....eeeeee...hhhhheeeeeeeeee....eeeeeee...eeeee........eeeee..........eeeeeeeeeee.....eeeee......eeeeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4odv H    1 EVKLVESGGGLVKLGGSLKLSCAASGFTFSSYYMSWVRQTPEKRLELVAAINSNGGNTYYPDTVKGLFTISRDNAKNTLYLQMSRLKSEDTALYYCTRLYGNYVRIHTMDYWGQGTSVTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSETVTCSVAHPASSTTVDKKLEPS  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||101       111       121       131       141       151       161       171       181       191       201       211  
                                                                              52A                            82A||               100A||||                                                                                                                 
                                                                                                              82B|                100B|||                                                                                                                 
                                                                                                               82C                 100C||                                                                                                                 
                                                                                                                                    100D|                                                                                                                 
                                                                                                                                     100E                                                                                                                 


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee...ee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4odv L    1 DIVLTQSTSSLSASLGDRVTITCRASQDIRNYLSWYQQRPDGTVKLLIYYTSKLHSGVPSRFSGSGSGTDYSLTITNLEQEDIATYFCQQGKTLPLYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  213
                                    10        20        30        40        50        60        70        80        90     |  99       109       119       129       139       149       159       169       179       189       199       209    
                                                                                                                         95A
   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 4ODV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ODV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ODV)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4ODV)

 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
    GP1  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    Z9M  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp H:130 - Thr H:131   [ RasMol ]  
    Cys H:128 - Gly H:129   [ RasMol ]  
    Glu H:1 - Val H:2   [ RasMol ]  
    Glu H:148 - Ser H:149   [ RasMol ]  
    Leu L:94 - Pro L:95   [ RasMol ]  
    Lys H:64 - Gly H:65   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Ser H:156 - Gly H:157   [ RasMol ]  
    Trp H:188 - Pro H:189   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

(-) 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
  4odv
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4ODV)

(-) Related Entries Specified in the PDB File

4ods 4odt 4odu 4odw 4ody 4odz 4oe0