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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ANTI-SSDNA ANTIGEN-BINDING FRAGMENT (FAB) BOUND TO 4-(2-HYDROXYETHYL)PIPERAZINE-1-ETHANESULFONIC ACID (HEPES)
 
Authors :  J. P. Schuermann, M. T. Henzl, S. L. Deutscher, J. J. Tanner
Date :  02 May 03  (Deposition) - 11 May 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Fab, Antibody, Anti-Dna Antibody, Autoantibody, Lupus, Hepes, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. P. Schuermann, M. T. Henzl, S. L. Deutscher, J. J. Tanner
Structure Of An Anti-Dna Fab Complexed With A Non-Dna Ligan Provides Insights Into Cross-Reactivity And Molecular Mimicry.
Proteins V. 57 269 2004
PubMed-ID: 15340914  |  Reference-DOI: 10.1002/PROT.20200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTIBODY LIGHT CHAIN FAB
    ChainsL, A
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCOMB3/6-HIS
    Expression System StrainDH12S
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 2 - ANTIBODY HEAVY CHAIN FAB
    ChainsH, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCOMB3/6-HIS
    Expression System StrainDH12S
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABHL
Biological Unit 1 (1x)  HL
Biological Unit 2 (1x)AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 33)

Asymmetric Unit (5, 33)
No.NameCountTypeFull Name
11PE4Ligand/IonPENTAETHYLENE GLYCOL
2EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3GOL16Ligand/IonGLYCEROL
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
5SO49Ligand/IonSULFATE ION
Biological Unit 1 (5, 19)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3GOL8Ligand/IonGLYCEROL
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
5SO46Ligand/IonSULFATE ION
Biological Unit 2 (4, 14)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3GOL8Ligand/IonGLYCEROL
4PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
5SO43Ligand/IonSULFATE ION

(-) Sites  (33, 33)

Asymmetric Unit (33, 33)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL H:2 , ARG H:94 , HOH H:1209BINDING SITE FOR RESIDUE SO4 H 801
02AC2SOFTWARETHR H:28 , SER H:31 , TYR H:32BINDING SITE FOR RESIDUE SO4 H 802
03AC3SOFTWARELYS H:58 , TYR H:100A , HOH H:1342 , GLY L:93 , THR L:94 , EPE L:901BINDING SITE FOR RESIDUE SO4 H 803
04AC4SOFTWARESER H:25 , GLY H:26 , TYR H:97 , HOH H:1311BINDING SITE FOR RESIDUE SO4 H 804
05AC5SOFTWARELYS A:52 , HOH A:1263 , SER H:158 , LEU H:159 , SER H:160 , SER H:161 , HOH H:1347BINDING SITE FOR RESIDUE SO4 H 805
06AC6SOFTWARELYS A:142 , TRP A:163 , THR A:164 , ASP A:165 , TYR A:173BINDING SITE FOR RESIDUE SO4 A 806
07AC7SOFTWAREGLY A:93 , THR A:94 , LYS B:58 , TYR B:100A , EPE B:902BINDING SITE FOR RESIDUE SO4 B 807
08AC8SOFTWARELYS H:73 , ARG L:108BINDING SITE FOR RESIDUE SO4 L 808
09AC9SOFTWARETYR B:27 , THR B:28 , TYR B:32 , HOH L:1364BINDING SITE FOR RESIDUE SO4 B 809
10BC1SOFTWAREARG H:98 , PRO H:99 , TYR H:100 , TYR H:100A , SO4 H:803 , TYR L:32 , HIS L:91 , TYR L:92 , HOH L:1294BINDING SITE FOR RESIDUE EPE L 901
11BC2SOFTWARETYR A:32 , HIS A:91 , TYR A:92 , PRO B:99 , TYR B:100 , TYR B:100A , SO4 B:807BINDING SITE FOR RESIDUE EPE B 902
12BC3SOFTWARETYR H:50 , ASN H:52 , TYR H:53 , ASN H:54 , TYR H:100 , PEG H:1202 , HOH H:1331 , HOH H:1339BINDING SITE FOR RESIDUE 1PE H 1001
13BC4SOFTWAREVAL B:33 , TYR B:50 , ASN B:52 , TYR B:53 , ASN B:54 , TYR B:100 , GOL B:1111 , HOH B:1223BINDING SITE FOR RESIDUE 1PE B 1002
14BC5SOFTWARETYR B:53 , SER L:31 , LYS L:52 , SER L:65 , GLY L:66 , SER L:67 , GLN L:70 , SER L:72BINDING SITE FOR RESIDUE 1PE L 1003
15BC6SOFTWARELEU B:11 , THR B:116 , PRO B:147 , GLU B:148 , PRO B:149 , PRO B:200 , ALA B:201 , HOH B:1229 , HOH B:1231 , HOH B:1240BINDING SITE FOR RESIDUE 1PE B 1004
16BC7SOFTWAREPRO B:14 , SER B:84 , ASP B:173 , HOH B:1221 , ILE L:150 , ASP L:151 , SER L:153 , ARG L:155 , HOH L:1223BINDING SITE FOR RESIDUE PEG L 1201
17BC8SOFTWARESER H:31 , TYR H:97 , 1PE H:1001BINDING SITE FOR RESIDUE PEG H 1202
18BC9SOFTWARELYS H:38 , GLU H:46 , LYS H:62 , PHE H:63 , HOH H:1279 , HOH H:1365BINDING SITE FOR RESIDUE GOL H 1101
19CC1SOFTWARELYS B:38 , GLU B:46 , LYS B:62 , PHE B:63 , GLU B:85 , HOH B:1151 , HOH B:1162BINDING SITE FOR RESIDUE GOL B 1102
20CC2SOFTWAREVAL A:15 , GLY A:16 , HOH A:1198 , SER L:31 , TYR L:32 , ASN L:50 , HOH L:1319 , HOH L:1337 , HOH L:1338BINDING SITE FOR RESIDUE GOL L 1103
21CC3SOFTWARELYS H:38 , GLN H:39 , LYS H:40 , GLN H:43 , GLY H:44 , GLU H:46 , HOH H:1328BINDING SITE FOR RESIDUE GOL H 1105
22CC4SOFTWAREPHE H:166 , PRO H:167 , THR H:176 , LEU H:177 , SER H:178 , HOH H:1215 , SER L:162 , SER L:176 , THR L:178BINDING SITE FOR RESIDUE GOL H 1106
23CC5SOFTWAREPRO L:8 , ALA L:9 , SER L:10 , HOH L:1277BINDING SITE FOR RESIDUE GOL L 1107
24CC6SOFTWAREVAL A:206 , LYS A:207 , GLU B:81BINDING SITE FOR RESIDUE GOL A 1108
25CC7SOFTWAREGLY H:127 , SER H:128 , ARG H:213 , PRO L:119 , PHE L:209 , ASN L:210 , ARG L:211 , HOH L:1311BINDING SITE FOR RESIDUE GOL L 1110
26CC8SOFTWARETYR B:97 , TYR B:100 , 1PE B:1002BINDING SITE FOR RESIDUE GOL B 1111
27CC9SOFTWAREARG A:108 , LYS B:73 , HOH L:1421BINDING SITE FOR RESIDUE GOL B 1112
28DC1SOFTWARETYR H:91 , GLN L:38 , LYS L:39 , GLY L:41 , LYS L:42 , HOH L:1247 , HOH L:1386BINDING SITE FOR RESIDUE GOL L 1115
29DC2SOFTWAREPRO A:8 , ALA A:9 , SER A:10 , HOH A:1200BINDING SITE FOR RESIDUE GOL A 1116
30DC3SOFTWARESER A:127 , HOH A:1169 , SER B:120 , TYR B:122 , SER H:120 , HOH H:1260 , HOH H:1291BINDING SITE FOR RESIDUE GOL B 1117
31DC4SOFTWAREGLN A:124 , SER A:127 , GLY A:129 , TYR B:122 , LYS B:143BINDING SITE FOR RESIDUE GOL A 1118
32DC5SOFTWAREGLN L:37 , GLY L:57 , PRO L:59 , HOH L:1205 , HOH L:1414BINDING SITE FOR RESIDUE GOL L 1119
33DC6SOFTWAREPHE A:83 , GLN A:166 , HOH A:1163 , TYR L:30BINDING SITE FOR RESIDUE GOL A 1120

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3B:22 -B:92
4B:140 -B:195
5H:22 -H:92
6H:140 -H:195
7L:23 -L:88
8L:134 -L:194

(-) Cis Peptide Bonds  (13, 13)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Thr L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:146 -Pro H:147
5Glu H:148 -Pro H:149
6Trp H:188 -Pro H:189
7Ser A:7 -Pro A:8
8Thr A:94 -Pro A:95
9Tyr A:140 -Pro A:141
10Arg B:98 -Pro B:99
11Phe B:146 -Pro B:147
12Glu B:148 -Pro B:149
13Trp B:188 -Pro B:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P7K)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGKC_MOUSE84-90
 
  2A:192-198
L:192-198
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGKC_MOUSE84-90
 
  1-
L:192-198
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGKC_MOUSE84-90
 
  1A:192-198
-

(-) Exons   (0, 0)

(no "Exon" information available for 1P7K)

(-) 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:214
 aligned with I6L978_MOUSE | I6L978 from UniProtKB/TrEMBL  Length:234

    Alignment length:214
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    
        I6L978_MOUSE     21 DIQLTQSPASLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQLLVYNAKTLADGVPSRFSGSRSGTQFSLKINSLQPEDFGSYYCQHHSGIPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  234
               SCOP domains d1p7ka1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1p7ka2 A:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1p7kA01 A:1-108 Immunoglobulins                                                                             1p7kA02 A:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1p7k A    1 ELQMTQSPASLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQLLVYNAKTLAEGVPSRFSGSGSGTQFSLKINSLQPEDFGSYYCQHHYGTPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    

Chain A from PDB  Type:PROTEIN  Length:214
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:214
                                                                                                                                        1                                                                                                         
                                     -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102    
          IGKC_MOUSE      - ------------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  106
               SCOP domains d1p7ka1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1p7ka2 A:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1p7kA01 A:1-108 Immunoglobulins                                                                             1p7kA02 A:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1p7k A    1 ELQMTQSPASLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQLLVYNAKTLAEGVPSRFSGSGSGTQFSLKINSLQPEDFGSYYCQHHYGTPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    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:217
 aligned with Q9JL75_MOUSE | Q9JL75 from UniProtKB/TrEMBL  Length:109

    Alignment length:217
                                     1                                                                                         92 93             109                                                                                                 
                                     1        11        21        31        41        51        61        71        81        91|  |    99       109         -         -         -         -         -         -         -         -         -       
        Q9JL75_MOUSE      - ---------ELVKPGASVKMSCKASGYTFTSYVMHWVKQKPGQGLEWIGYINPYNDGTKYNEKFKGKATLTSDKSSSTAYMELSSLTSEDSAVYYCARDGN--YRGFDYWGQGTTLTVSS-------------------------------------------------------------------------------------------------    -
               SCOP domains d1p7kb1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                          d1p7kb2 B:114-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                   SCOP domains
               CATH domains 1p7kB01 B:1-113 Immunoglobulins                                                                                         1p7kB02 B:114-211 Immunoglobulins                                                             --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1p7k B    1 QVKLLESGPELVKPGASVKMSCKASGYTFTSYVMHWVKQKPGQGLEWIGYINPYNDGTKYNEKFKGKATLTSDKSSSTAYMELSSLTSEDSAVYYCVRGGYRPYYAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123    || 137       147       157       167       177       187       197       207       
                                                                              52A                            82A||               100A||                         128|                                                                                 
                                                                                                              82B|                100B|                          133                                                                                 
                                                                                                               82C                 100C                                                                                                              

Chain H from PDB  Type:PROTEIN  Length:220
 aligned with Q9JL75_MOUSE | Q9JL75 from UniProtKB/TrEMBL  Length:109

    Alignment length:220
                                     1                                                                                         92 93             109                                                                                                    
                                     1        11        21        31        41        51        61        71        81        91|  |    99       109         -         -         -         -         -         -         -         -         -         -
        Q9JL75_MOUSE      - ---------ELVKPGASVKMSCKASGYTFTSYVMHWVKQKPGQGLEWIGYINPYNDGTKYNEKFKGKATLTSDKSSSTAYMELSSLTSEDSAVYYCARDGN--YRGFDYWGQGTTLTVSS----------------------------------------------------------------------------------------------------    -
               SCOP domains d1p7kh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                          d1p7kh2 H:114-215 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains -1p7kH01 H:2-113 Immunoglobulins                                                                                        1p7kH02 H:114-211 Immunoglobulins                                                               ---- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1p7k H    1 QVKLLESGPELVKPGASVKMSCKASGYTFTSYVMHWVKQKPGQGLEWIGYINPYNDGTKYNEKFKGKATLTSDKSSSTAYMELSSLTSEDSAVYYCVRGGYRPYYAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAANSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC  215
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123      |135       145       155       165       175       185       195       205       215
                                                                              52A                            82A||               100A||                           130|                                                                                  
                                                                                                              82B|                100B|                            133                                                                                  
                                                                                                               82C                 100C                                                                                                                 

Chain L from PDB  Type:PROTEIN  Length:213
 aligned with I6L978_MOUSE | I6L978 from UniProtKB/TrEMBL  Length:234

    Alignment length:213
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   
        I6L978_MOUSE     21 DIQLTQSPASLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQLLVYNAKTLADGVPSRFSGSRSGTQFSLKINSLQPEDFGSYYCQHHSGIPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  233
               SCOP domains d1p7kl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1p7kl2 L:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1p7kL01 L:1-108 Immunoglobulins                                                                             1p7kL02 L:109-212 Immunoglobulins                                                                       - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhheeeeeee...........eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1p7k L    1 ELQMTQSPASLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQLLVYNAKTLAEGVPSRFSGSGSGTQFSLKINSLQPEDFGSYYCQHHYGTPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   

Chain L from PDB  Type:PROTEIN  Length:213
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:213
                                                                                                                                        1                                                                                                        
                                     -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102   
          IGKC_MOUSE      - ------------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  105
               SCOP domains d1p7kl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1p7kl2 L:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1p7kL01 L:1-108 Immunoglobulins                                                                             1p7kL02 L:109-212 Immunoglobulins                                                                       - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhheeeeeee...........eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1p7k L    1 ELQMTQSPASLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQLLVYNAKTLAEGVPSRFSGSGSGTQFSLKINSLQPEDFGSYYCQHHYGTPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   

   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

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
1a1p7kL02L:109-212
1b1p7kH02H:114-211
1c1p7kB02B:114-211
1d1p7kA02A:109-211
1e1p7kH01H:2-113
1f1p7kB01B:1-113
1g1p7kA01A:1-108
1h1p7kL01L:1-108

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1P7K)

(-) Gene Ontology  (24, 31)

Asymmetric Unit(hide GO term definitions)
Chain A,L   (IGKC_MOUSE | P01837)
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:0030183    B cell differentiation    The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
    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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A,L   (I6L978_MOUSE | I6L978)

Chain B,H   (Q9JL75_MOUSE | Q9JL75)

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 Related Entries

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

UniProtKB/Swiss-Prot
        IGHG1_MOUSE | P018681ahw 1ai1 1bm3 1clo 1ct8 1dba 1dbb 1dbj 1dbk 1dbm 1emt 1fbi 1fdl 1fns 1gpo 1k4d 1kel 1kem 1mf2 1mlc 1n5y 1n6q 1ntl 1oak 1opg 1p2c 1r0a 1r3i 1r3j 1r3k 1r3l 1rih 1seq 1t2q 1yed 2aty 2b2x 2dbl 3zo0
        IGKC_MOUSE | P0183715c8 1a0q 1a3l 1ahw 1ai1 1aif 1c12 1cf8 1cfn 1cfq 1cfs 1cft 1cic 1ck0 1ct8 1dqj 1dqm 1dqq 1e4w 1e4x 1ehl 1emt 1f11 1fai 1fbi 1fdl 1fe8 1fgn 1fj1 1fl3 1fns 1frg 1fsk 1gpo 1hh6 1hh9 1hi6 1i8m 1iai 1igy 1jnl 1jnn 1jrh 1k4c 1k4d 1kb5 1kc5 1kcr 1kcs 1kcu 1kcv 1ken 1kno 1lo0 1mf2 1mh5 1mlb 1mlc 1n5y 1n6q 1nby 1nbz 1ndg 1ndm 1oak 1ob1 1orq 1ors 1osp 1ots 1ott 1otu 1p2c 1psk 1q9o 1q9w 1qgc 1r0a 1r24 1r3i 1r3j 1r3k 1r3l 1rih 1ruq 1rur 1s5h 1seq 1t03 1t4k 1ub5 1ub6 1uwx 1xf2 1xf3 1xf4 1xgp 1xgq 1xgu 25c8 2a6d 2a6k 2adf 2adj 2ajs 2aju 2ajv 2ajx 2ajy 2ajz 2ak1 2bob 2boc 2ck0 2f19 2fr4 2g5b 2h8p 2hg5 2hrp 2mpa 2nr6 2q76 2r1w 2r1y 2r23 2r2b 2uyl 2v17 2v7h 2vc2 2vdk 2vdl 2vdm 2vdn 2vdo 2vdp 2vdq 2vdr 2vl5 2vq1 2vwe 2w60 2w65 2w9d 2w9e 2z91 2z92 2z93 2zjs 35c8 3bae 3bgf 3bkc 3bkj 3bkm 3bpc 3bqu 3bsz 3bt2 3bz4 3c5s 3c6s 3cfb 3cfc 3cfd 3cfe 3ck0 3cle 3clf 3cmo 3cvh 3cvi 3d9a 3ejz 3eot 3f7v 3f7y 3fb6 3hfm 4kk5 4kk8 4qnp 4zxb 6fab
UniProtKB/TrEMBL
        I6L978_MOUSE | I6L9783vrl
        Q9JL75_MOUSE | Q9JL752ddq

(-) Related Entries Specified in the PDB File

1i8m CRYSTAL STRUCTURE OF A RECOMBINANT ANTI-SINGLE-STRANDED DNA ANTIBODY FRAGMENT COMPLEXED WITH DT5