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 :  CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF A HUMAN MONOCLONAL IGM COLD AGGLUTININ
 
Authors :  J. G. Carvalho, A. Cauerhff, F. Goldbaum, J. Leoni, I. Polikarpov
Date :  11 Sep 99  (Deposition) - 14 Sep 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.83
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Immunoglobulin, Autoantibody, Cold Agglutinin, Human Igm Fab Fragment (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Cauerhff, B. C. Braden, J. G. Carvalho, R. Aparicio, I. Polikarpov, J. Leoni, F. A. Goldman
Three-Dimensional Structure Of The Fab Fragment From A Human Igm Cold Agglutinin
J. Immunol. V. 165 6422 2000
PubMed-ID: 11086081
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IGM KAPPA CHAIN V-III (KAU COLD AGGLUTININ)
    Cell: B-LYMPHOCYTE
    Cellular Location: EXTRACELLULAR
    Chains: A, C
    Fragment: FAB FRAGMENT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: FAB FRAGMENT WAS PREPARED BY DIGESTION OF MONOCLONAL IGM KAU PURIFIED FROM PATIENT WITH AIHA.
 
Molecule 2 - IGM FAB REGION IV-J(H4)-C (KAU COLD AGGLUTININ)
    Cell: B-LYMPHOCYTE
    Cellular Location: EXTRACELLULAR
    Chains: B, D
    Fragment: FAB FRAGMENT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: FAB FRAGMENT WAS PREPARED BY DIGESTION OF MONOCLONAL IGM KAU PURIFIED FROM PATIENT WITH AIHA.

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:164 , ASN B:166 , ASP B:203 , FUC B:302BINDING SITE FOR RESIDUE NAG B 301
2AC2SOFTWARETHR B:202 , ASP B:203 , NAG B:301BINDING SITE FOR RESIDUE FUC B 302
3AC3SOFTWAREASN D:166 , FUC D:302BINDING SITE FOR RESIDUE NAG D 301
4AC4SOFTWARETHR D:202 , ASP D:203 , NAG D:301BINDING SITE FOR RESIDUE FUC D 302

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3A:214 -B:134
4B:22 -B:95
5B:148 -B:208
6C:23 -C:88
7C:134 -C:194
8C:214 -D:134
9D:22 -D:95
10D:148 -D:208

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ser A:7 -Pro A:8
2Ser A:94 -Pro A:95
3Tyr A:140 -Pro A:141
4Leu B:154 -Pro B:155
5Ser C:7 -Pro C:8
6Ser C:94 -Pro C:95
7Tyr C:140 -Pro C:141
8Leu D:154 -Pro D:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1QLR)

(-) 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:215
 aligned with Q6PJF2_HUMAN | Q6PJF2 from UniProtKB/TrEMBL  Length:235

    Alignment length:215
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     
         Q6PJF2_HUMAN    21 EIVLTQSPATLSLSPGERATLSCRASQIVSSAYLAWYQQKPGQAPRLLMFGSSSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSQGTFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 235
               SCOP domains d1qlra1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                  d1qlra2 A:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1qlrA01 A:1-108 Immunoglobulins                                                                              1qlrA02 A:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee...hhhh.eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeee............eeee.......eeeee..hhhhhhh.eeeeeeeee.......eeeeee........eeeee...........eeeeeeeehhhhhhh.eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qlr A   1 EIVLTQSPATLSLSPGERATLSCGASQSVSSNYLAWYQQKPGQAPRLLIYDASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 214
                                    10        20        30|       39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209     
                                                        30A                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains d1qlrb1 B:1-120 Immunoglobulin heavy chain variable domain, VH                                                          d1qlrb2 B:121-225 Immunoglobulin heavy chain mu constant domain 1, CH1-mu                 SCOP domains
               CATH domains 1qlrB01 B:1-120 Immunoglobulins                                                                                         1qlrB02 B:121-222 Immunoglobulins                                                     --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........eeeeeeee........eeeeee.....eeeeeee.....eee...hhh.eeeeee....eeeeee...hhhhheeeeeee................eee..........eeeee....eeeeeeeee.....eeeeee........eee...eee..eeeeeeeee.....eeeeeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qlr B   1 EVQLQQWGAGLLKPSETLSLTCAVYGGSFSDYYWSWIRQPPGKGLEWIGEINHSGSTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARPPHDTSGHYWNYWGQGTLVTVSSGSASAPTLFPLVSCVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVLRGGKYAATSQVLLPTDEHVVCKVQHPNGNKEKNVPLPV 225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  149       159       169       179       189    || 206       216         
                                                                                                                                                               134|                                               194|                       
                                                                                                                                                                144                                                202                       


Chain C from PDB  Type:PROTEIN  Length:215
 aligned with Q6PJF2_HUMAN | Q6PJF2 from UniProtKB/TrEMBL  Length:235

    Alignment length:215
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     
         Q6PJF2_HUMAN    21 EIVLTQSPATLSLSPGERATLSCRASQIVSSAYLAWYQQKPGQAPRLLMFGSSSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSQGTFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 235
               SCOP domains d1qlrc1 C:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                  d1qlrc2 C:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1qlrC01 C:1-108 Immunoglobulins                                                                              1qlrC02 C:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee...hhhh.eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeee............eeee.......eeeee..hhhhhhh.eeeeeeeee.......eeeeee........eeeee...........eeeeeeeehhhhhhh.eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qlr C   1 EIVLTQSPATLSLSPGERATLSCGASQSVSSNYLAWYQQKPGQAPRLLIYDASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 214
                                    10        20        30|       39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209     
                                                        30A                                                                                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains d1qlrd1 D:1-120 Immunoglobulin heavy chain variable domain, VH                                                          d1qlrd2 D:121-225 Immunoglobulin heavy chain mu constant domain 1, CH1-mu                 SCOP domains
               CATH domains 1qlrD01 D:1-120 Immunoglobulins                                                                                         1qlrD02 D:121-223 Immunoglobulins                                                      -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........eeeeeeee........eeeeee.....eeeeeee.....eee...hhh.eeeeee....eeeeee...hhhhheeeeeee................eee..........eeeee....eeeeeee.......eeeee.........eee...eee..eeeeeeeee......eeeeee.....eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qlr D   1 EVQLQQWGAGLLKPSETLSLTCAVYGGSFSDYYWSWIRQPPGKGLEWIGEINHSGSTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARPPHDTSGHYWNYWGQGTLVTVSSGSASAPTLFPLVSCVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVLRGGKYAATSQVLLPTDEHVVCKVQHPNGNKEKNVPLPV 225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  149       159       169       179       189    || 206       216         
                                                                                                                                                               134|                                               194|                       
                                                                                                                                                                144                                                202
   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, 8)

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

(-) CATH Domains  (1, 8)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
Human (Homo sapiens) (912)
1a1qlrA02A:109-211
1b1qlrA01A:1-108
1c1qlrC01C:1-108
1d1qlrB01B:1-120
1e1qlrD01D:1-120
1f1qlrD02D:121-223
1g1qlrB02B:121-222
1h1qlrC02C:109-211

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

 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
    FUC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ 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
    Leu B:154 - Pro B:155   [ RasMol ]  
    Leu D:154 - Pro D:155   [ RasMol ]  
    Ser A:7 - Pro A:8   [ RasMol ]  
    Ser A:94 - Pro A:95   [ RasMol ]  
    Ser C:7 - Pro C:8   [ RasMol ]  
    Ser C:94 - Pro C:95   [ RasMol ]  
    Tyr A:140 - Pro A:141   [ RasMol ]  
    Tyr C:140 - Pro C: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
  1qlr
    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
  Q6PJF2_HUMAN | Q6PJF2
    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
  Q6PJF2_HUMAN | Q6PJF2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        Q6PJF2_HUMAN | Q6PJF2: 4ypg
UniProtKB/TrEMBL
        Q6PJF2_HUMAN | Q6PJF2: 1dn0 2agj 3eyf 3eyo

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1QLR)