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(-) Description

Title :  STRUCTURE OF THE FAB FRAGMENT FROM A HUMAN IGM COLD AGGLUTININ
 
Authors :  A. Cauerhff, B. Braden, J. G. Carvalho, J. Leoni, I. Polikarpov, F. Goldbaum
Date :  15 Dec 99  (Deposition) - 24 Jan 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Fab, Igm, Antibody, Cold Agglutinin, Human, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Cauerhff, B. C. Braden, J. G. Carvalho, R. Aparicio, I. Polikarpov, J. Leoni, F. A. Goldbaum
Three-Dimensional Structure Of The Fab 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 COLD AGGLUTININ (LIGHT CHAIN)
    Chains: A, C
    Fragment: FAB FRAGMENT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - IGM-KAPPA COLD AGGLUTININ (HEAVY CHAIN)
    Chains: B, D
    Fragment: FAB FRAGMENT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1DN0)

(-) Sites  (0, 0)

(no "Site" information available for 1DN0)

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:23 -A:89
2A:135 -A:195
3A:215 -B:134
4B:22 -B:95
5B:148 -B:208
6C:23 -C:89
7C:135 -C:195
8C:215 -D:134
9D:22 -D:95
10D:148 -D:208

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Ser A:95 -Pro A:96
3Tyr A:141 -Pro A:142
4Leu B:154 -Pro B:155
5Ser C:7 -Pro C:8
6Ser C:95 -Pro C:96
7Tyr C:141 -Pro C:142
8Leu D:154 -Pro D:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DN0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1DN0)

(-) Exons   (0, 0)

(no "Exon" information available for 1DN0)

(-) 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: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 d1dn0a1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1dn0a2 A:108-215 Immunoglobulin light chain kappa constant domain, CL-kappa                                 SCOP domains
               CATH domains 1dn0A01 A:1-109 Immunoglobulins                                                                              1dn0A02 A:110-212 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee...hhhh.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dn0 A   1 EIVLTQSPATLSLSPGERATLSCGASQSVSSNYLAWYQQKPGQAPRLLIYDASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     


Chain B from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d1dn0b1 B:1-120 Immunoglobulin heavy chain variable domain, VH                                                          d1dn0b2 B:121-225 Immunoglobulin heavy chain mu constant domain 1, CH1-mu                        SCOP domains
               CATH domains 1dn0B01 B:1-120 Immunoglobulins                                                                                         1dn0B02 B:121-222 Immunoglobulins                                                            --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee......eeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeee...........ee...eeeee........eeeeee.....eeeeeeeeee.....eeeeee....ee..eee...eee..eeeeeeeeee........eeeeeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dn0 B   1 EVQLQQWGAGLLKPSETLSLTCAVYGGSFSDYYWSWIRQPPGKGLEWIGEINHSGSTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARPPHDTSGHYWNYWGQGTLVTVSSGSASAPTLFPLVSCTSSVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVLRGGKYAATSQVLLPSKDVTDEHVVCKVQHPNGNKEKNVPLPV 225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  146       156       166       176       186       196 ||    209       219      
                                                                                                                                                               134|                                                      198|                       
                                                                                                                                                                141                                                       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 d1dn0c1 C:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1dn0c2 C:108-215 Immunoglobulin light chain kappa constant domain, CL-kappa                                 SCOP domains
               CATH domains 1dn0C01 C:1-109 Immunoglobulins                                                                              1dn0C02 C:110-212 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee...hhhh.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dn0 C   1 EIVLTQSPATLSLSPGERATLSCGASQSVSSNYLAWYQQKPGQAPRLLIYDASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     


Chain D from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d1dn0d1 D:1-120 Immunoglobulin heavy chain variable domain, VH                                                          d1dn0d2 D:121-225 Immunoglobulin heavy chain mu constant domain 1, CH1-mu                         SCOP domains
               CATH domains 1dn0D01 D:1-120 Immunoglobulins                                                                                         1dn0D02 D:121-222 Immunoglobulins                                                             --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee......eeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeee...........ee...eeeee........eeeeee...eeeeeeeeee.....eeeeee....ee........eee..eeeeeeeeeehhhhhh.....eeeeeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dn0 D   1 EVQLQQWGAGLLKPSETLSLTCAVYGGSFSDYYWSWIRQPPGKGLEWIGEINHSGSTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARPPHDTSGHYWNYWGQGTLVTVSSGSASAPTLFPLVSCSVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVLRGGKYAATSQVLLPSKDVMAGTDEHVVCKVQHPNGNKEKNVPLPV 225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  148       158       168       178       188       198       208       218       
                                                                                                                                                               134|                                                                                  
                                                                                                                                                                143
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
Human (Homo sapiens) (912)
1a1dn0A02A:110-212
1b1dn0A01A:1-109
1c1dn0C01C:1-109
1d1dn0B01B:1-120
1e1dn0D01D:1-120
1f1dn0D02D:121-222
1g1dn0B02B:121-222
1h1dn0C02C:110-212

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DN0)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1DN0)

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 Related Entries

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

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        Q6PJF2_HUMAN | Q6PJF2: 4ypg
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