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(-) Description

Title :  STRUCTURE OF CATALYTIC ELIMINATION ANTIBODY 13G5 FROM A CRYSTAL IN SPACE GROUP P2(1)
 
Authors :  E. W. Debler, I. A. Wilson
Date :  31 Mar 06  (Deposition) - 06 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  A (1x),B (1x),H (1x),L (1x)
Biol. Unit 4:  A (1x),B (1x),H (1x),L (1x)
Biol. Unit 5:  A (1x),B (1x),H (1x),L (1x)
Biol. Unit 6:  A (1x),B (1x),H (1x),L (1x)
Biol. Unit 7:  A (1x),B (1x),H (1x),L (1x)
Biol. Unit 8:  A (1x),B (1x),H (1x),L (1x)
Biol. Unit 9:  A (1x),B (1x)
Keywords :  Immunoglobulin, Catalytic Antibody, Elimination, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Muller, E. W. Debler, M. Steinmann, F. P. Seebeck, I. A. Wilson, D. Hilvert
Bifunctional Catalysis Of Proton Transfer At An Antibody Active Site.
J. Am. Chem. Soc. V. 129 460 2007
PubMed-ID: 17226987  |  Reference-DOI: 10.1021/JA066578B

(-) Compounds

Molecule 1 - CATALYTIC ELIMINATION ANTIBODY 13G5 LIGHT CHAIN
    Chains: L, A
    Fragment: FAB FRAGMENT
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - CATALYTIC ELIMINATION ANTIBODY 13G5 HEAVY CHAIN
    Chains: H, B
    Fragment: FAB FRAGMENT
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABHL
Biological Unit 1 (1x):   HL
Biological Unit 2 (1x): AB  
Biological Unit 3 (1x): A (1x)B (1x)H (1x)L (1x)
Biological Unit 4 (1x): A (1x)B (1x)H (1x)L (1x)
Biological Unit 5 (1x): A (1x)B (1x)H (1x)L (1x)
Biological Unit 6 (1x): A (1x)B (1x)H (1x)L (1x)
Biological Unit 7 (1x): A (1x)B (1x)H (1x)L (1x)
Biological Unit 8 (1x): A (1x)B (1x)H (1x)L (1x)
Biological Unit 9 (1x): A (1x)B (1x)  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 11)

Asymmetric Unit (1, 11)
No.NameCountTypeFull Name
1ZN11Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 7 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 8 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 9 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS L:27DBINDING SITE FOR RESIDUE ZN L 213
02AC2SOFTWAREASP L:60BINDING SITE FOR RESIDUE ZN L 214
03AC3SOFTWAREHIS H:172 , HOH H:232 , ASN L:138 , ASP L:167BINDING SITE FOR RESIDUE ZN L 215
04AC4SOFTWAREASP L:151 , HIS L:189 , HOH L:222BINDING SITE FOR RESIDUE ZN L 216
05AC5SOFTWAREASP H:35 , HIS H:95 , HOH H:231BINDING SITE FOR RESIDUE ZN H 229
06AC6SOFTWAREHIS H:102BINDING SITE FOR RESIDUE ZN H 230
07AC7SOFTWAREASN A:138 , ASP A:167 , HIS B:172BINDING SITE FOR RESIDUE ZN B 229
08AC8SOFTWAREASP A:151 , HIS A:189 , HOH A:214BINDING SITE FOR RESIDUE ZN A 213
09AC9SOFTWAREHIS L:93 , HOH L:219 , HOH L:223BINDING SITE FOR RESIDUE ZN L 217
10BC1SOFTWAREASP B:35 , HIS B:95 , HOH B:240BINDING SITE FOR RESIDUE ZN B 230
11BC2SOFTWAREHIS B:102BINDING SITE FOR RESIDUE ZN B 231

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3B:22 -B:92
4B:142 -B:208
5H:22 -H:92
6H:142 -H:208
7L:23 -L:88
8L:134 -L:194

(-) Cis Peptide Bonds  (11, 11)

Asymmetric Unit
No.Residues
1Thr L:7 -Pro L:8
2Leu L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:148 -Pro H:149
5Glu H:150 -Pro H:151
6Trp H:199 -Pro H:200
7Thr A:7 -Pro A:8
8Tyr A:140 -Pro A:141
9Phe B:148 -Pro B:149
10Glu B:150 -Pro B:151
11Trp B:199 -Pro B:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GJZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GJZ)

(-) Exons   (0, 0)

(no "Exon" information available for 2GJZ)

(-) 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:217
 aligned with Q65ZC0_MOUSE | Q65ZC0 from UniProtKB/TrEMBL  Length:219

    Alignment length:217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
        Q65ZC0_MOUSE      1 ELVMTQSPLSLSVSLGDQASISCRSSQSLVHTNGNTYLHWYLQKPGLSPKLLIYIVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPGTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRG  217
               SCOP domains d2gjza1 A:1-108 automated matches                                                                                d2gjza2 A:109-212 automated matches                                                                      SCOP domains
               CATH domains 2gjzA01 A:1-108 Immunoglobulins                                                                                  -2gjzA02 A:110-209 Immunoglobulins                                                                   --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeee.............eeeee...eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2gjz A    1 ELVMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKINRVEAEDLGVYYCFQGSHLPPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  212
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       
                                                     27A||||                                                                                                                                                                                         
                                                      27B|||                                                                                                                                                                                         
                                                       27C||                                                                                                                                                                                         
                                                        27D|                                                                                                                                                                                         
                                                         27E                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2gjzB01 B:1-114 Immunoglobulins                                                                                           2gjzB02 B:115-228 Immunoglobulins                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee......eeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeee.........eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee.........eeeee.hhhh.eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2gjz B    1 QVQLKESGPGLVAPSQSLSITCTVSGFSLTNYGVDWVRQPPGKGLEWVGVIWSGGSTNYNSALMSRLSISKDNSKSQVFLKMNSLQTDDTAVYYCAKHWGGYYIPYGMDHWGQGTTVTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPEPVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPR  228
                                    10        20        30        40        50        60        70        80  |||   87        97   ||||102       112       122       134       144       154|||    169|      180|      192   || |204 ||    215       227 
                                                                                                            82A||               100A||||                           130|                  154|||    169|      180|          196| || 206|            223|  
                                                                                                             82B|                100B|||                            133                   156||     171       183           198 ||  208             226  
                                                                                                              82C                 100C||                                                   157|                               200|                       
                                                                                                                                   100D|                                                    162                                202                       
                                                                                                                                    100E                                                                                                                 


Chain H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2gjzH01 H:1-114 Immunoglobulins                                                                                           2gjzH02 H:115-228 Immunoglobulins                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee......eeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeee.........eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2gjz H    1 QVQLKESGPGLVAPSQSLSITCTVSGFSLTNYGVDWVRQPPGKGLEWVGVIWSGGSTNYNSALMSRLSISKDNSKSQVFLKMNSLQTDDTAVYYCAKHWGGYYIPYGMDHWGQGTTVTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPEPVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPR  228
                                    10        20        30        40        50        60        70        80  |||   87        97   ||||102       112       122       134       144       154|||    169|      180|      192   || |204 ||    215       227 
                                                                                                            82A||               100A||||                           130|                  154|||    169|      180|          196| || 206|            223|  
                                                                                                             82B|                100B|||                            133                   156||     171       183           198 ||  208             226  
                                                                                                              82C                 100C||                                                   157|                               200|                       
                                                                                                                                   100D|                                                    162                                202                       
                                                                                                                                    100E                                                                                                                 


Chain L from PDB  Type:PROTEIN  Length:217
 aligned with Q65ZC0_MOUSE | Q65ZC0 from UniProtKB/TrEMBL  Length:219

    Alignment length:217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
        Q65ZC0_MOUSE      1 ELVMTQSPLSLSVSLGDQASISCRSSQSLVHTNGNTYLHWYLQKPGLSPKLLIYIVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPGTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRG  217
               SCOP domains d2gjzl1 L:1-108 automated matches                                                                                d2gjzl2 L:109-212 automated matches                                                                      SCOP domains
               CATH domains 2gjzL01 L:1-108 Immunoglobulins                                                                                  -2gjzL02 L:110-209 Immunoglobulins                                                                   --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee......eeee.............eeeee...eeeeee...hhhhh.eeeeee......ee...eeeeee......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2gjz L    1 ELVMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKINRVEAEDLGVYYCFQGSHLPPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  212
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       
                                                     27A||||                                                                                                                                                                                         
                                                      27B|||                                                                                                                                                                                         
                                                       27C||                                                                                                                                                                                         
                                                        27D|                                                                                                                                                                                         
                                                         27E
   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, 4)

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)
1a2gjzA02A:110-209
1b2gjzB02B:115-228
1c2gjzH02H:115-228
1d2gjzA01A:1-108
1e2gjzL01L:1-108
1f2gjzB01B:1-114
1g2gjzH01H:1-114
1h2gjzL02L:110-209

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GJZ)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,L   (Q65ZC0_MOUSE | Q65ZC0)

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  2gjz
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  Q65ZC0_MOUSE | Q65ZC0
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 Related Entries

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

UniProtKB/Swiss-Prot
        IGG2B_MOUSE | P01867: 1cbv 1cf8 1cic 1etz 1fj1 1fl3 1hq4 1mam 1nbv 1osp 1ub5 1ub6 1ynk 1ynl 1ztx 2gk0 2q8a 2q8b 2rgs 3cfd 3cfe
        Q65ZC0_MOUSE | Q65ZC0: 2g60
UniProtKB/TrEMBL
        Q65ZC0_MOUSE | Q65ZC0: 1i9i 1i9j 1l7t 1lo2 1lo3 1lo4 1t66 2gk0

(-) Related Entries Specified in the PDB File

2gk0 STRUCTURE OF CATALYTIC ELIMINATION ANTIBODY 13G5 FROM A TWINNED CRYSTAL IN SPACE GROUP C2