Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  FV IGE SPE-7 IN COMPLEX WITH ALIZARIN RED
 
Authors :  L. C. James, P. Roversi, D. Tawfik
Date :  21 Jan 03  (Deposition) - 15 Jan 04  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym. Unit :  H,I,J,K,L,M,N,O
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  I,M  (1x)
Biol. Unit 3:  J,N  (1x)
Biol. Unit 4:  K,O  (1x)
Keywords :  Immune System, Antibody-Complex, Antibody, Allergy, Ige, Conformational Diversity, Multispecificity (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. C. James, P. Roversi, D. Tawfik
Antibody Multispecificity Mediated By Conformational Diversity
Science V. 299 1362 2003
PubMed-ID: 12610298  |  Reference-DOI: 10.1126/SCIENCE.1079731

(-) Compounds

Molecule 1 - IMMUNOGLOBULING E
    ChainsL, M, N, O
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentFV, RESIDUES 1-110
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 2 - IMMUNOGLOBULIN E
    ChainsH, I, J, K
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentFV, RESIDUES 1-122
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsEXPRESSED AS RECOMBINANT FV IN E.COLI

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit HIJKLMNO
Biological Unit 1 (1x)H   L   
Biological Unit 2 (1x) I   M  
Biological Unit 3 (1x)  J   N 
Biological Unit 4 (1x)   K   O

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 46)

Asymmetric Unit (6, 46)
No.NameCountTypeFull Name
1AZN4Ligand/IonALIZARIN RED
2CAC2Ligand/IonCACODYLATE ION
3CL8Ligand/IonCHLORIDE ION
4DMS24Ligand/IonDIMETHYL SULFOXIDE
5EDO2Ligand/Ion1,2-ETHANEDIOL
6NA6Ligand/IonSODIUM ION
Biological Unit 1 (4, 15)
No.NameCountTypeFull Name
1AZN1Ligand/IonALIZARIN RED
2CAC1Ligand/IonCACODYLATE ION
3CL-1Ligand/IonCHLORIDE ION
4DMS12Ligand/IonDIMETHYL SULFOXIDE
5EDO1Ligand/Ion1,2-ETHANEDIOL
6NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1AZN1Ligand/IonALIZARIN RED
2CAC-1Ligand/IonCACODYLATE ION
3CL-1Ligand/IonCHLORIDE ION
4DMS-1Ligand/IonDIMETHYL SULFOXIDE
5EDO-1Ligand/Ion1,2-ETHANEDIOL
6NA-1Ligand/IonSODIUM ION
Biological Unit 3 (4, 15)
No.NameCountTypeFull Name
1AZN1Ligand/IonALIZARIN RED
2CAC1Ligand/IonCACODYLATE ION
3CL-1Ligand/IonCHLORIDE ION
4DMS12Ligand/IonDIMETHYL SULFOXIDE
5EDO1Ligand/Ion1,2-ETHANEDIOL
6NA-1Ligand/IonSODIUM ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1AZN1Ligand/IonALIZARIN RED
2CAC-1Ligand/IonCACODYLATE ION
3CL-1Ligand/IonCHLORIDE ION
4DMS-1Ligand/IonDIMETHYL SULFOXIDE
5EDO-1Ligand/Ion1,2-ETHANEDIOL
6NA-1Ligand/IonSODIUM ION

(-) Sites  (45, 45)

Asymmetric Unit (45, 45)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR H:115 , HOH H:2065 , HIS L:44BINDING SITE FOR RESIDUE CAC H 201
02AC2SOFTWAREGLN L:6 , GLY L:102 , GLY L:103 , HOH L:2062BINDING SITE FOR RESIDUE NA H 903
03AC3SOFTWAREDMS H:304 , CL N:913 , HOH N:2010 , HOH N:2012BINDING SITE FOR RESIDUE NA I 903
04AC4SOFTWARETHR J:115 , HOH J:2063 , HIS N:44BINDING SITE FOR RESIDUE CAC J 201
05AC5SOFTWAREGLN N:6 , GLY N:102 , GLY N:103 , HOH N:2064BINDING SITE FOR RESIDUE NA J 903
06AC6SOFTWAREHOH H:2026 , EDO J:401 , PHE L:89 , CL L:913 , HOH L:2035BINDING SITE FOR RESIDUE NA L 901
07AC7SOFTWARETRP H:47 , LEU L:98 , PHE L:100BINDING SITE FOR RESIDUE CL L 911
08AC8SOFTWAREGLN H:82BINDING SITE FOR RESIDUE CL L 912
09AC9SOFTWAREGLY L:102 , NA L:901BINDING SITE FOR RESIDUE CL L 913
10BC1SOFTWARETYR J:102 , GLY J:103 , THR M:17 , VAL M:18 , THR M:19 , CL M:913 , HOH M:2007BINDING SITE FOR RESIDUE NA M 903
11BC2SOFTWARENA M:903BINDING SITE FOR RESIDUE CL M 913
12BC3SOFTWAREEDO H:401 , PHE N:89 , CL N:913 , HOH N:2034BINDING SITE FOR RESIDUE NA N 901
13BC4SOFTWARETRP J:47 , LEU N:98 , PHE N:100BINDING SITE FOR RESIDUE CL N 911
14BC5SOFTWAREGLN J:82BINDING SITE FOR RESIDUE CL J 912
15BC6SOFTWARENA I:903 , GLY N:102 , NA N:901BINDING SITE FOR RESIDUE CL N 913
16BC7SOFTWAREARG H:50 , ASP H:52 , GLY H:57 , HOH H:2031 , HOH H:2066 , GLY O:70BINDING SITE FOR RESIDUE DMS H 300
17BC8SOFTWARETYR H:60 , LYS H:65 , HOH H:2033 , HOH H:2038 , PRO L:61 , ARG L:63BINDING SITE FOR RESIDUE DMS H 301
18BC9SOFTWAREPRO H:41 , ALA H:92 , DMS H:304 , HOH H:2062BINDING SITE FOR RESIDUE DMS H 302
19CC1SOFTWARESER H:17 , GLN H:82 , SER L:65BINDING SITE FOR RESIDUE DMS H 303
20CC2SOFTWAREPRO H:41 , DMS H:302 , EDO H:401 , NA I:903BINDING SITE FOR RESIDUE DMS H 304
21CC3SOFTWARETYR H:102 , GLU O:7BINDING SITE FOR RESIDUE DMS H 305
22CC4SOFTWAREHOH H:2068 , DMS L:300 , DMS L:304 , GLU O:16BINDING SITE FOR RESIDUE DMS H 306
23CC5SOFTWAREDMS H:304 , ILE N:87 , NA N:901 , HOH N:2034BINDING SITE FOR RESIDUE EDO H 401
24CC6SOFTWARETRP H:33 , HIS H:35 , ARG H:50 , LYS H:59 , MET H:99 , TYR H:105 , TYR L:34 , ASN L:36 , TRP L:93 , LEU O:68 , ILE O:69 , GLY O:70 , HOH O:2028BINDING SITE FOR RESIDUE AZN H 500
25CC7SOFTWARETRP I:33 , HIS I:35 , ARG I:50 , LYS I:59 , MET I:99 , TYR I:105 , TYR M:34 , ASN M:36 , TRP M:93BINDING SITE FOR RESIDUE AZN I 500
26CC8SOFTWAREARG J:50 , ASP J:52 , GLY J:57 , HOH J:2029 , HOH J:2064 , GLY M:70BINDING SITE FOR RESIDUE DMS J 300
27CC9SOFTWARETYR J:60 , LYS J:65 , HOH J:2031 , HOH J:2035 , PRO N:61 , ARG N:63BINDING SITE FOR RESIDUE DMS J 301
28DC1SOFTWAREPRO J:41 , ALA J:92 , DMS J:304 , HOH J:2060BINDING SITE FOR RESIDUE DMS J 302
29DC2SOFTWARESER J:17 , GLN J:82 , SER N:65BINDING SITE FOR RESIDUE DMS J 303
30DC3SOFTWAREPRO J:41 , DMS J:302 , EDO J:401BINDING SITE FOR RESIDUE DMS J 304
31DC4SOFTWARETYR J:102 , GLU M:7BINDING SITE FOR RESIDUE DMS J 305
32DC5SOFTWAREHOH J:2066 , GLU M:16 , DMS N:300 , DMS N:304BINDING SITE FOR RESIDUE DMS J 306
33DC6SOFTWAREDMS J:304 , ILE L:87 , NA L:901 , HOH L:2035BINDING SITE FOR RESIDUE EDO J 401
34DC7SOFTWARETRP J:33 , HIS J:35 , ARG J:50 , LYS J:59 , MET J:99 , TYR J:105 , LEU M:68 , ILE M:69 , GLY M:70 , HOH M:2027 , TYR N:34 , ASN N:36 , TRP N:93BINDING SITE FOR RESIDUE AZN J 500
35DC8SOFTWARETRP K:33 , HIS K:35 , ARG K:50 , LYS K:59 , MET K:99 , TYR K:105 , TYR O:34 , ASN O:36 , TRP O:93BINDING SITE FOR RESIDUE AZN K 500
36DC9SOFTWARESER H:85 , DMS H:306 , ASN L:54 , ASN L:55 , ARG L:56 , DMS L:304BINDING SITE FOR RESIDUE DMS L 300
37EC1SOFTWAREGLN L:39 , PRO L:61 , HOH L:2060 , HOH L:2067BINDING SITE FOR RESIDUE DMS L 301
38EC2SOFTWAREVAL L:4 , PHE L:100 , GLY L:102BINDING SITE FOR RESIDUE DMS L 302
39EC3SOFTWAREGLY L:52 , ASN L:54 , ASN L:55 , HOH L:2032BINDING SITE FOR RESIDUE DMS L 303
40EC4SOFTWARESER H:66 , DMS H:306 , ARG L:56 , ALA L:57 , VAL L:60 , DMS L:300BINDING SITE FOR RESIDUE DMS L 304
41EC5SOFTWARESER J:85 , DMS J:306 , ASN N:54 , ASN N:55 , ARG N:56 , DMS N:304BINDING SITE FOR RESIDUE DMS N 300
42EC6SOFTWARELYS J:65 , GLN N:39 , PRO N:61 , HOH N:2061 , HOH N:2069BINDING SITE FOR RESIDUE DMS N 301
43EC7SOFTWAREVAL N:4 , PHE N:100 , GLY N:102BINDING SITE FOR RESIDUE DMS N 302
44EC8SOFTWAREGLY N:52 , ASN N:54 , ASN N:55 , HOH N:2044BINDING SITE FOR RESIDUE DMS N 303
45EC9SOFTWARESER J:66 , DMS J:306 , ARG N:56 , ALA N:57 , PRO N:58 , VAL N:60 , DMS N:300BINDING SITE FOR RESIDUE DMS N 304

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1H:22 -H:96
2I:22 -I:96
3J:22 -J:96
4K:22 -K:96
5L:22 -L:90
6M:22 -M:90
7N:22 -N:90
8O:22 -O:90

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OAR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1OAR)

(-) 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 H from PDB  Type:PROTEIN  Length:122
 aligned with HVM07_MOUSE | P01751 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:122
                                                                                                                                                 139  
                                    29        39        49        59        69        79        89        99       109       119       129       139  
          HVM07_MOUSE    20 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTLTVSS--   -
               SCOP domains d1oarh_ H: Immunoglobulin heavy chain variable domain, VH                                                                  SCOP domains
               CATH domains 1oarH00 H:1-122 Immunoglobulins                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee.....eeeee...eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oar H   1 EVQLQQSGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNGGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARMWYYGTYYFDYWGQGTTLTVSSAA 122
                                    10        20        30        40        50        60        70        80        90       100       110       120  

Chain I from PDB  Type:PROTEIN  Length:88
 aligned with HVM07_MOUSE | P01751 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:103
                                    42        52        62        72        82        92       102       112       122       132   
          HVM07_MOUSE    33 PGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTL 135
               SCOP domains d1oari_ I: Immunoglobulin h    eavy cha    in variable doma    in, VH                                   SCOP domains
               CATH domains 1oarI00 I:14-116 Immunoglob    ulins                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.........eeeeeee.----.eeeeee.----.eee.......eeee.----.eeeeee...---...eeeeeeee.....eeeee...ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1oar I  14 PGASVKLSCKASGYTFTSYWMHWVKQR----LEWIGRID----GTKYNEKFKSKATLTV----STAYMQLSSL---DSAVYYCARMWYYGTYYFDYWGQGTTL 116
                                    23        33      |  - |      |-   |    63        |-   |    83  |   | 93       103       113   
                                                     40   45     52   57             72   77       86  90                          

Chain J from PDB  Type:PROTEIN  Length:122
 aligned with HVM07_MOUSE | P01751 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:122
                                                                                                                                                 139  
                                    29        39        49        59        69        79        89        99       109       119       129       139  
          HVM07_MOUSE    20 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTLTVSS--   -
               SCOP domains d1oarj_ J: Immunoglobulin heavy chain variable domain, VH                                                                  SCOP domains
               CATH domains 1oarJ00 J:1-122 Immunoglobulins                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee.....eeeee...eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oar J   1 EVQLQQSGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNGGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARMWYYGTYYFDYWGQGTTLTVSSAA 122
                                    10        20        30        40        50        60        70        80        90       100       110       120  

Chain K from PDB  Type:PROTEIN  Length:82
 aligned with HVM07_MOUSE | P01751 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:103
                                    42        52        62        72        82        92       102       112       122       132   
          HVM07_MOUSE    33 PGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTL 135
               SCOP domains d1oark_ K:       Immunoglob    ulin hea    vy chain variabl    e domain,    VH                          SCOP domains
               CATH domains 1oarK00 K:      14-116 Immu    noglobul    ins                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.------...eeeeeee.----.eeeeee.----.eee.......eeee.----..eeeee...---...eeeeeeee.....eeeee...ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1oar K  14 PGASVKLSCK------TSYWMHWVKQR----LEWIGRID----GTKYNEKFKSKATLTV----STAYMQLSSL---DSAVYYCARMWYYGTYYFDYWGQGTTL 116
                                    23      | 33      |  - |      |-   |    63        |-   |    83  |   | 93       103       113   
                                    23     30        40   45     52   57             72   77       86  90                          

Chain L from PDB  Type:PROTEIN  Length:108
 aligned with LV1B_MOUSE | P01724 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:108
                                    30        40        50        60        70        80        90       100       110       120        
           LV1B_MOUSE    21 AVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQQKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVL 128
               SCOP domains d1oarl_ L: Immunoglobulin light chain lambda variable domain, VL-lambda                                      SCOP domains
               CATH domains 1oarL00 L:2-109 Immunoglobulins                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee..eeee....eeeeeeee.....hhhhh.eeeeee...eeeeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeeeee..eeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1oar L   2 AVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHLVFGGGTKLTVL 109
                                    11        21        31        41        51        61        71        81        91       101        

Chain M from PDB  Type:PROTEIN  Length:103
 aligned with LV1B_MOUSE | P01724 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:107
                                    31        41        51        61        71        81        91       101       111       121       
           LV1B_MOUSE    22 VVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQQKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVL 128
               SCOP domains d1oarm_ M: Immunoglob    ulin light chain lambda variable domain, VL-lambda                                 SCOP domains
               CATH domains 1oarM00 M:3-109 Immun    oglobulins                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..eeee....eeeeeee----..hhhhh.eeeeee...eeeeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeeeee..eeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1oar M   3 VVTQESALTTSPGETVTLTCR----AVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHLVFGGGTKLTVL 109
                                    12        22|    |  32        42        52        62        72        82        92       102       
                                               23   28                                                                                 

Chain N from PDB  Type:PROTEIN  Length:108
 aligned with LV1B_MOUSE | P01724 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:108
                                    30        40        50        60        70        80        90       100       110       120        
           LV1B_MOUSE    21 AVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQQKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVL 128
               SCOP domains d1oarn_ N: Immunoglobulin light chain lambda variable domain, VL-lambda                                      SCOP domains
               CATH domains 1oarN00 N:2-109 Immunoglobulins                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee..eeee....eeeeeeee.....hhhhh.eeeeee...eeeeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeeeee..eeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1oar N   2 AVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHLVFGGGTKLTVL 109
                                    11        21        31        41        51        61        71        81        91       101        

Chain O from PDB  Type:PROTEIN  Length:106
 aligned with LV1B_MOUSE | P01724 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:107
                                    31        41        51        61        71        81        91       101       111       121       
           LV1B_MOUSE    22 VVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQQKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVL 128
               SCOP domains d1oaro_ O: Immunoglobuli n light chain lambda variable domain, VL-lambda                                    SCOP domains
               CATH domains 1oarO00 O:3-109 Immunogl obulins                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eeee....eeeeeeee..-..hhhhh.eeeeee...eeeeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeeeee..eeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1oar O   3 VVTQESALTTSPGETVTLTCRSST-AVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHLVFGGGTKLTVL 109
                                    12        22   | |  32        42        52        62        72        82        92       102       
                                                  26 |                                                                                 
                                                    28                                                                                 

   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  (2, 8)

Asymmetric Unit

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
1a1oarH00H:1-122
1b1oarO00O:3-109
1c1oarM00M:3-109
1d1oarL00L:2-109
1e1oarN00N:2-109
1f1oarJ00J:1-122
1g1oarI00I:14-116
1h1oarK00K:14-116

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 13)

Asymmetric Unit(hide GO term definitions)
Chain H,I,J,K   (HVM07_MOUSE | P01751)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
    GO:0034987    immunoglobulin receptor binding    Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule.
biological process
    GO:0050853    B cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
    GO:0006958    complement activation, classical pathway    Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0006911    phagocytosis, engulfment    The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
    GO:0006910    phagocytosis, recognition    The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
    GO:0050871    positive regulation of B cell activation    Any process that activates or increases the frequency, rate or extent of B cell activation.
cellular component
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0042571    immunoglobulin complex, circulating    An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.

Chain L,M,N,O   (LV1B_MOUSE | P01724)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.

 Visualization

(-) Interactive Views

Asymmetric 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
    AZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CAC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DMS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
    CC6  [ RasMol ]  +environment [ RasMol ]
    CC7  [ RasMol ]  +environment [ RasMol ]
    CC8  [ RasMol ]  +environment [ RasMol ]
    CC9  [ RasMol ]  +environment [ RasMol ]
    DC1  [ RasMol ]  +environment [ RasMol ]
    DC2  [ RasMol ]  +environment [ RasMol ]
    DC3  [ RasMol ]  +environment [ RasMol ]
    DC4  [ RasMol ]  +environment [ RasMol ]
    DC5  [ RasMol ]  +environment [ RasMol ]
    DC6  [ RasMol ]  +environment [ RasMol ]
    DC7  [ RasMol ]  +environment [ RasMol ]
    DC8  [ RasMol ]  +environment [ RasMol ]
    DC9  [ RasMol ]  +environment [ RasMol ]
    EC1  [ RasMol ]  +environment [ RasMol ]
    EC2  [ RasMol ]  +environment [ RasMol ]
    EC3  [ RasMol ]  +environment [ RasMol ]
    EC4  [ RasMol ]  +environment [ RasMol ]
    EC5  [ RasMol ]  +environment [ RasMol ]
    EC6  [ RasMol ]  +environment [ RasMol ]
    EC7  [ RasMol ]  +environment [ RasMol ]
    EC8  [ RasMol ]  +environment [ RasMol ]
    EC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1oar)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1oar
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  HVM07_MOUSE | P01751
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  LV1B_MOUSE | P01724
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  HVM07_MOUSE | P01751
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  LV1B_MOUSE | P01724
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        HVM07_MOUSE | P017511a6u 1a6v 1a6w 1ngp 1ngq 1nqb 1oaq 1oau 1oax 1oay 1oaz 1ocw 2bjm
        LV1B_MOUSE | P017241a6u 1a6v 1a6w 1dl7 1oaq 1oau 1oax 1oay 1oaz 1ocw 1q0y 2bjm

(-) Related Entries Specified in the PDB File

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