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 :  S25-2 FAB UNLIGANDED 1
 
Authors :  H. P. Nguyen, N. O. Seto, C. R. Mackenzie, L. Brade, P. Kosma, H. Brade, S. V. Evans
Date :  25 Aug 03  (Deposition) - 27 Jan 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Antigen-Binding Fragment, Fab, Anti-Carbohydrate, Anti-Lps, Antibody, Immunoglobulin, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. P. Nguyen, N. O. Seto, C. R. Mackenzie, L. Brade, P. Kosma, H. Brade, S. V. Evans
Germline Antibody Recognition Of Distinct Carbohydrate Epitopes.
Nat. Struct. Biol. V. 10 1019 2003
PubMed-ID: 14625588  |  Reference-DOI: 10.1038/NSB1014
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - S25-2 FAB (IGG1K) LIGHT CHAIN
    Chains: A
    Fragment: LIGHT CHAIN KAPPA
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - S25-2 FAB (IGG1K) HEAVY CHAIN
    Chains: B
    Fragment: HEAVY CHAIN G1
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:96 , PHE A:97 , TRP B:47BINDING SITE FOR RESIDUE MG A 214
2AC2SOFTWAREASN A:137 , ASP A:166 , LYS A:168 , HOH A:548 , HIS B:162BINDING SITE FOR RESIDUE MG A 215
3AC3SOFTWAREGLN A:6 , SER A:7 , MET A:21 , SER A:22 , THR A:101BINDING SITE FOR RESIDUE MG A 216
4AC4SOFTWAREHIS A:188 , HOH A:404 , HOH A:435BINDING SITE FOR RESIDUE MG A 217

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:88
2A:133 -A:193
3B:22 -B:92
4B:138 -B:193

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser A:7 -Pro A:8
2Tyr A:139 -Pro A:140
3Phe B:144 -Pro B:145
4Glu B:146 -Pro B:147
5Trp B:186 -Pro B:187

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q9K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q9K)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q9K)

(-) 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:219
                                                                                                                                                                                                                                                            
               SCOP domains d1q9ka1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                       d1q9ka2 A:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1q9kA01 A:1-107 Immunoglobulins                                                                                  1q9kA02 A:108-210 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1q9k A    1 DIVMSQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTITSVQAEDLAVYYCKQSYNLRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  213
                                    10        20        30||||||  34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204         
                                                        30A|||||                                                                                                                                                                                       
                                                         30B||||                                                                                                                                                                                       
                                                          30C|||                                                                                                                                                                                       
                                                           30D||                                                                                                                                                                                       
                                                            30E|                                                                                                                                                                                       
                                                             30F                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                               
               SCOP domains d1q9kb1 B:1-111 Immunoglobulin heavy chain variable domain, VH                                                            d1q9kb2 B:112-211 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1q9kB01 B:1-111 Immunoglobulins                                                                                           1q9kB02 B:112-210 Immunoglobulins                                                                  - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeee......eeeeee.hhhhh..eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee..............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1q9k B    1 EVKLVESGGGLVQSGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKANGYTTEYSPSVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCARDHDGYYERFSYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR  211
                                    10        20        30        40        50  ||||| 55        65        75       |84        94      100D|      109       119       129       139       149       159       169       179       189       199       209  
                                                                              52A||||                            82A               100A||||                                                                                                               
                                                                               52B|||                                               100B|||                                                                                                               
                                                                                52C||                                                100C||                                                                                                               
                                                                                 52D|                                                 100D|                                                                                                               
                                                                                  52E                                                  100E
   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  (4, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Q9K)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1Q9K)

 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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu B:146 - Pro B:147   [ RasMol ]  
    Phe B:144 - Pro B:145   [ RasMol ]  
    Ser A:7 - Pro A:8   [ RasMol ]  
    Trp B:186 - Pro B:187   [ RasMol ]  
    Tyr A:139 - Pro A:140   [ 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
  1q9k
    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 1Q9K)

(-) Related Entries Specified in the PDB File

1q9l S25-2 FAB UNLIGANDED, DIFFERENT CRYSTAL FORM
1q9o S45-18 FAB, UNLIGANDED
1q9q S25-2 LIGANDED WITH A(2-8)-A(2-4) KDO TRISACCHARIDE
1q9r S25-2 LIGANDED WITH A(2-8) KDO DISACCHARIDE
1q9t S25-2 LIGANDED WITH A(2-4) KDO DISACCHARIDE
1q9v S25-2 LIGANDED WITH KDO MONOSACCHARIDE
1q9w S45-18 FAB PENTASACCHARIDE BISPHOSPHATE COMPLEX