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(-) Description

Title :  CRYSTAL STRUCTURE OF A QUORUM-QUENCHING ANTIBODY IN COMPLEX WITH AN N-ACYL-L-HOMOSERINE LACTONE ANALOG
 
Authors :  E. W. Debler, I. A. Wilson
Date :  07 Nov 06  (Deposition) - 08 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.18
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  A,B,H,L  (1x)
Keywords :  Immunoglobulin, Antibody, Fab, Hapten Complex, Quorum Sensing, Homoserine Lactone, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. W. Debler, G. F. Kaufmann, R. N. Kirchdoerfer, J. M. Mee, K. D. Janda, I. A. Wilson
Crystal Structures Of A Quorum-Quenching Antibody.
J. Mol. Biol. V. 368 1392 2007
PubMed-ID: 17400249  |  Reference-DOI: 10.1016/J.JMB.2007.02.081

(-) Compounds

Molecule 1 - MURINE ANTIBODY FAB RS2-1G9 LAMBDA LIGHT CHAIN
    Chains: L, A
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: PURIFIED FROM ASCITIC FLUID
    Strain: BALB/C
 
Molecule 2 - MURINE ANTIBODY FAB RS2-1G9 IGG1 HEAVY CHAIN
    Chains: H, B
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: PURIFIED FROM ASCITIC FLUID
    Strain: BALB/C

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABHL
Biological Unit 1 (1x):   HL
Biological Unit 2 (1x): AB  
Biological Unit 3 (1x): ABHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1OHM2Ligand/Ion3-OXO-N-[(3S)-2-OXOPYRROLIDIN-3-YL]DODECANAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1OHM1Ligand/Ion3-OXO-N-[(3S)-2-OXOPYRROLIDIN-3-YL]DODECANAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1OHM1Ligand/Ion3-OXO-N-[(3S)-2-OXOPYRROLIDIN-3-YL]DODECANAMIDE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1OHM2Ligand/Ion3-OXO-N-[(3S)-2-OXOPYRROLIDIN-3-YL]DODECANAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:189 , TRP H:33 , HIS H:35 , GLY H:95 , SER H:96 , ASN H:100 , ASN H:100A , GLY H:100C , TRP H:100D , PHE H:100E , TYR L:32 , ASN L:34 , TRP L:96BINDING SITE FOR RESIDUE OHM H 1001
2AC2SOFTWAREASN A:34 , TRP A:91 , TRP A:96 , TRP B:33 , HIS B:35 , GLY B:95 , SER B:96 , ASN B:100A , GLY B:100C , TRP B:100D , PHE B:100EBINDING SITE FOR RESIDUE OHM B 1002

(-) 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  (8, 8)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2NTF)

(-) 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:211
                                                                                                                                                                                                                                                    
               SCOP domains d2ntfa1 A:1-108 automated matches                                                                              d2ntfa2 A:109-211 automated matches                                                                  SCOP domains
               CATH domains 2ntfA01 A:1-107 Immunoglobulins                                                                               2ntfA02 A:108-211 Immunoglobulins                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...eeee.....eeeeeee.....hhhhh.eeeeee...eeeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeeee....eee...eeeee...........ee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeeehhhhhhh.eeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ntf A    1 QAVVTQESALTTSPGETVTLTCRSSTGAVTTRNYANWVQEKPDHFFTGLIGDTNNRAPGVPARFSGSLIGHKAALTITGAQTEDESVYFCALWYSNHWVFGGGTKLTVLGQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSYLTLTAGAWERHSSYSCQVTHEGHTVEKSLSR  211
                                    11        21      ||28        38        48        58        68        78        88        98       107       117       127       137       147       157       167||     178       188       198 ||    210 
                                    9|              27A||                                                                            106A                                                           168|                           200|        
                                    11               27B|                                                                                                                                            170                            203        
                                                      27C                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:222
 aligned with Q99LC4_MOUSE | Q99LC4 from UniProtKB/TrEMBL  Length:463

    Alignment length:222
                                                                                                                             118   123                                                                                                                    
                                                                                                                           117 | 122 |                                                                                                                    
                                    29        39        49        59        69        79        89        99       109       118   | | 127       137       147       157       167       177       187       197       207       217       227       237  
        Q99LC4_MOUSE     20 QVQLQQSGAELARPGASVRLSCKASGYTFTGYGVSWVKQRTGQGLEWVGEIYPGSGNTYYSEKFKGKATLTTDKSSSTAYMHLSSLTSEDSAVYFCAR-SSYYS-YDLFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR  239
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2ntfB01 B:1-114 Immunoglobulins                                                                                            2ntfB02 B:115-228 Immunoglobulins                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhh.eeeeeeee......eeeeeee....eeee.hhhh..eeee......eeeeee...hhhhheeeeeeeeee.........ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2ntf B    1 QVQLQQSGSELVRPGASVKLSCKASGYTFTTYWIHWVKQRPGQGLEWIGTIYPGSDNTYYDEKFKNKATLTVDTSSSTAFMQLSSLTSEDSAVYFCTRGSLYYNNYGWFGYWGQGTLVTVSAAKTTPPSVYPLAPGSNAASQSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLTSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPR  228
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||101       111       121       133       143       153||||   169       181       191    || 203  ||   214       226  
                                                                              52A                            82A||               100A||||                           130|                  154|||  167|     177|             196| || 206|            223|  
                                                                                                              82B|                100B|||                            133                   156||   169      180              198 ||  208             226  
                                                                                                               82C                 100C||                                                   157|                               200|                       
                                                                                                                                    100D|                                                    162                                202                       
                                                                                                                                     100E                                                                                                                 


Chain H from PDB  Type:PROTEIN  Length:222
 aligned with Q99LC4_MOUSE | Q99LC4 from UniProtKB/TrEMBL  Length:463

    Alignment length:222
                                                                                                                             118   123                                                                                                                    
                                                                                                                           117 | 122 |                                                                                                                    
                                    29        39        49        59        69        79        89        99       109       118   | | 127       137       147       157       167       177       187       197       207       217       227       237  
        Q99LC4_MOUSE     20 QVQLQQSGAELARPGASVRLSCKASGYTFTGYGVSWVKQRTGQGLEWVGEIYPGSGNTYYSEKFKGKATLTTDKSSSTAYMHLSSLTSEDSAVYFCAR-SSYYS-YDLFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR  239
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2ntfH01 H:1-114 Immunoglobulins                                                                                            2ntfH02 H:115-228 Immunoglobulins                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhh.eeeeeeee......eeeeeee....eeee.hhhh..eeee......eeeeee...hhhhheeeeeeeeee.........ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2ntf H    1 QVQLQQSGSELVRPGASVKLSCKASGYTFTTYWIHWVKQRPGQGLEWIGTIYPGSDNTYYDEKFKNKATLTVDTSSSTAFMQLSSLTSEDSAVYFCTRGSLYYNNYGWFGYWGQGTLVTVSAAKTTPPSVYPLAPGSNAASQSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLTSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPR  228
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||101       111       121       133       143       153||||   169       181       191    || 203  ||   214       226  
                                                                              52A                            82A||               100A||||                           130|                  154|||  167|     177|             196| || 206|            223|  
                                                                                                              82B|                100B|||                            133                   156||   169      180              198 ||  208             226  
                                                                                                               82C                 100C||                                                   157|                               200|                       
                                                                                                                                    100D|                                                    162                                202                       
                                                                                                                                     100E                                                                                                                 


Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains d2ntfl1 L:1-108 automated matches                                                                              d2ntfl2 L:109-211 automated matches                                                                  SCOP domains
               CATH domains 2ntfL01 L:1-107 Immunoglobulins                                                                               2ntfL02 L:108-211 Immunoglobulins                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eeee.....eeeeeee.....hhhhh.eeeeee...eeeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeeee....eee...eeeee...........ee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeeehhhhhhh.eeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ntf L    1 QAVVTQESALTTSPGETVTLTCRSSTGAVTTRNYANWVQEKPDHFFTGLIGDTNNRAPGVPARFSGSLIGHKAALTITGAQTEDESVYFCALWYSNHWVFGGGTKLTVLGQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSYLTLTAGAWERHSSYSCQVTHEGHTVEKSLSR  211
                                    11        21      ||28        38        48        58        68        78        88        98       107       117       127       137       147       157       167||     178       188       198 ||    210 
                                    9|              27A||                                                                            106A                                                           168|                           200|        
                                    11               27B|                                                                                                                                            170                            203        
                                                      27C
   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)
1a2ntfB02B:115-228
1b2ntfH02H:115-228
1c2ntfB01B:1-114
1d2ntfH01H:1-114
1e2ntfA01A:1-107
1f2ntfL01L:1-107
1g2ntfA02A:108-211
1h2ntfL02L:108-211

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2NTF)

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  2ntf
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  Q99LC4_MOUSE | Q99LC4
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q99LC4_MOUSE | Q99LC4: 1afv 3hkf
UniProtKB/TrEMBL
        Q99LC4_MOUSE | Q99LC4: 1ae6 1e6j 1f58 1gig 1jhk 1jnl 1jnn 2a1w 2vir 2vis 2vit 4q0x

(-) Related Entries Specified in the PDB File

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