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(-) Description

Title :  S25-2 FAB UNLIGANDED 2
 
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 :  2.28
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x)
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) HEAVY CHAIN
    Chains: B, D
    Fragment: FAB HEAVY CHAIN G1
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - S25-2 FAB (IGG1K) LIGHT CHAIN
    Chains: A, C
    Fragment: FAB LIGHT CHAIN KAPPA
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1MG7Ligand/IonMAGNESIUM ION
2ZN3Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:184 , HIS A:188 , HOH A:690 , HOH A:702BINDING SITE FOR RESIDUE ZN A 214
02AC2SOFTWAREGLU C:184 , HIS C:188 , HOH C:674 , HOH C:688BINDING SITE FOR RESIDUE ZN C 214
03AC3SOFTWAREASP C:1BINDING SITE FOR RESIDUE ZN C 215
04AC4SOFTWARETHR A:96 , PHE A:97 , TRP B:47 , HOH B:362BINDING SITE FOR RESIDUE MG B 212
05AC5SOFTWARETHR C:96 , PHE C:97 , TRP D:47 , HOH D:504BINDING SITE FOR RESIDUE MG C 216
06AC6SOFTWARELYS C:89 , ARG C:95 , HOH C:631 , ASP D:95BINDING SITE FOR RESIDUE MG C 217
07AC7SOFTWAREASP A:166 , LYS A:168 , HOH A:694 , HOH A:701 , HIS B:162 , HOH B:303 , HOH B:695BINDING SITE FOR RESIDUE MG A 215
08AC8SOFTWAREASP C:166 , LYS C:168 , HOH C:314 , HIS D:162 , HOH D:351BINDING SITE FOR RESIDUE MG C 218
09AC9SOFTWAREGLU B:1 , HOH B:530 , ASP D:171BINDING SITE FOR RESIDUE MG D 212
10BC1SOFTWARELYS C:148 , ASP C:150 , GLY C:151 , SER C:190 , THR C:192BINDING SITE FOR RESIDUE MG C 219

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:133 -A:193
3B:22 -B:92
4B:138 -B:193
5C:23 -C:88
6C:133 -C:193
7D:22 -D:92
8D:138 -D:193

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Phe B:144 -Pro B:145
2Glu B:146 -Pro B:147
3Trp B:186 -Pro B:187
4Phe D:144 -Pro D:145
5Glu D:146 -Pro D:147
6Trp D:186 -Pro D:187
7Ser A:7 -Pro A:8
8Tyr A:139 -Pro A:140
9Ser C:7 -Pro C:8
10Tyr C:139 -Pro C:140

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q9L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q9L)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q9L)

(-) 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:219
                                                                                                                                                                                                                                                            
               SCOP domains d1q9la1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                       d1q9la2 A:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1q9lA01 A:1-107 Immunoglobulins                                                                                  1q9lA02 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..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1q9l 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 d1q9lb1 B:1-111 Immunoglobulin heavy chain variable domain, VH                                                            d1q9lb2 B:112-211 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1q9lB01 B:1-111 Immunoglobulins                                                                                           1q9lB02 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........eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1q9l 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                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d1q9lc1 C:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                       d1q9lc2 C:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1q9lC01 C:1-107 Immunoglobulins                                                                                  1q9lC02 C:108-210 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1q9l C    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 D from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                               
               SCOP domains d1q9ld1 D:1-111 Immunoglobulin heavy chain variable domain, VH                                                            d1q9ld2 D:112-211 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1q9lD01 D:1-111 Immunoglobulins                                                                                           1q9lD02 D:112-210 Immunoglobulins                                                                  - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee..eee.....eeeeee....hhhhheeeeeee......eeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeeee..............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1q9l D    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, 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)
(-)
House mouse (Mus musculus) (616)
1a1q9lA02A:108-210
1b1q9lB02B:112-210
1c1q9lD02D:112-210
1d1q9lA01A:1-107
1e1q9lC01C:1-107
1f1q9lB01B:1-111
1g1q9lD01D:1-111
1h1q9lC02C:108-210

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Q9L)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1Q9L)

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  1q9l
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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1Q9L)

(-) Related Entries Specified in the PDB File

1q9k 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