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(-) Description

Title :  CRYSTAL STRUCTURE (A) OF U.V.-IRRADIATED CATIONIC CYCLIZATION ANTIBODY 4C6 FAB AT PH 4.6 WITH A DATA SET COLLECTED IN-HOUSE.
 
Authors :  X. Zhu, P. Wentworth Jr. , A. D. Wentworth, A. Eschenmoser, R. A. Lerner I. A. Wilson
Date :  11 Dec 03  (Deposition) - 02 Mar 04  (Release) - 05 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin, Catalytic Antibody, Water Oxidation, Amino Acid Modification, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Zhu, P. Wentworth Jr. , A. D. Wentworth, A. Eschenmoser, R. A. Lerner, I. A. Wilson
Probing The Antibody-Catalyzed Water-Oxidation Pathway At Atomic Resolution.
Proc. Natl. Acad. Sci. Usa V. 110 2247 2004
PubMed-ID: 14982995  |  Reference-DOI: 10.1073/PNAS.0307311101
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IMMUNOGLOBULIN IGG2A, LIGHT CHAIN
    Chains: L
    Fragment: FAB
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: 129G1X+
 
Molecule 2 - IMMUNOGLOBULIN IGG2A, HEAVY CHAIN
    Chains: H
    Fragment: FAB
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: 129G1X+

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
14HT1Mod. Amino Acid4-HYDROXYTRYPTOPHAN
2ACT1Ligand/IonACETATE ION
3BEZ1Ligand/IonBENZOIC ACID
4GHG1Mod. Amino Acid(2S,4S)-2,5-DIAMINO-4-HYDROXY-5-OXOPENTANOIC ACID (NON-PREFERRED NAME)
5GOL5Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU H:95 , TRP H:103 , HOH H:712 , ASN L:34 , LEU L:36BINDING SITE FOR RESIDUE ACT H 611
2AC2SOFTWAREALA H:34 , ASN H:35A , TYR H:50 , LEU H:95 , LEU H:96 , PRO H:230 , PHE L:32 , TRP L:89 , GLY L:91BINDING SITE FOR RESIDUE BEZ H 601
3AC3SOFTWARELYS H:44 , LEU H:45 , THR L:97 , PHE L:98 , HOH L:624BINDING SITE FOR RESIDUE GOL H 621
4AC4SOFTWAREPHE H:174 , PRO H:175 , THR H:186 , SER H:188 , SER L:176 , THR L:178BINDING SITE FOR RESIDUE GOL L 622
5AC5SOFTWAREARG H:71 , ASP H:72 , THR H:73 , LEU L:54BINDING SITE FOR RESIDUE GOL H 623
6AC6SOFTWAREVAL H:12 , GLN H:16 , SER H:17 , ASP H:32 , TYR H:53 , TRP H:97 , HOH H:627 , HOH H:644BINDING SITE FOR RESIDUE GOL H 624
7AC7SOFTWAREVAL H:121 , TYR H:122 , SER H:215 , LYS H:221 , HOH H:666 , HOH H:727 , GLU L:123BINDING SITE FOR RESIDUE GOL H 625

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:142 -H:208
3L:23 -L:88
4L:134 -L:194
5L:214 -H:128

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Phe 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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RU9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RU9)

(-) Exons   (0, 0)

(no "Exon" information available for 1RU9)

(-) Sequences/Alignments

Asymmetric/Biological 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:222
                                                                                                                                                                                                                                                               
               SCOP domains d1ru9h1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                         d1ru9h2 H:114-231 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                         SCOP domains
               CATH domains 1ru9H01 H:1-113 Immunoglobulins                                                                                        1ru9H02 H:114-227 Immunoglobulins                                                                  ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeeee.....eeeeeeee....eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeee.......ee...eeeee........eeeee..hhhhhh..eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1ru9 H    1 RVQLQqSGPGLVKPSQSLSLTCTVTGYSITSDFAWNWIRQFPGNKLEWMGYINYSGFTSHNPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYYCAGLLWYDGGAGSWGQGTLVTVSAAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPT  231
                                 |  10        20        30     |  39        49        59        69        79   |||  86        96    || 104       114       124     ||136       146       157|      172       184       194 || || 206|      217     ||229  
                                 6-GHG                       35A                                             82A||               100A|                           130|                  154|||    169|      180|          196| || 206|            223|     
                                                                                                              82B|                100B                            133                   156||     171       183           198 ||  208             226     
                                                                                                               82C                                                                       157|                               200|                          
                                                                                                                                                                                          162                                202                          


Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d1ru9l1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1ru9l2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1ru9L01 L:1-108 Immunoglobulins                                                                                  1ru9L02 L:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ru9 L    1 DVVMTQSPKTISVTIGQPASISCKSSQRLLNSNGKTFLNWLLQRPGQSPKRLIYLGTKLDSGVPDRFTGSGSGTDFTLKISRVEAEDLGVYYCWQGTHFPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSwTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205         
                                                     27A||||                                                                                                                                     163-4HT                                               
                                                      27B|||                                                                                                                                                                                           
                                                       27C||                                                                                                                                                                                           
                                                        27D|                                                                                                                                                                                           
                                                         27E
   Legend:   → Mismatch (orange background)
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  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, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1RU9)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        GCAM_MOUSE | P01865: 1axt 1dqj 1e4w 1egj 1flr 1fpt 1ggb 1ggc 1kb5 1lo0 1nby 1nbz 1nca 1ncb 1ncc 1ncd 1ncw 1nd0 1ndg 1ndm 1orq 1plg 1rua 1ruk 1rul 1rum 1rup 1yee 3fo9 3j3p 4fab 4zxb

(-) Related Entries Specified in the PDB File

1ncw SAME NATIVE PROTEIN
1nd0 SAME NATIVE PROTEIN COMPLEX WITH TRANSITION STATE ANALOG
1rua CRYSTAL STRUCTURE OF U.V.-IRRADIATED CATIONIC CYCLIZATION ANTIBODY 4C6 FAB AT PH 4.6 WITH A DATA SET COLLECTED AT SSRL BEAMLINE 11-1.
1ruk CRYSTAL STRUCTURE OF NATIVE CATIONIC CYCLIZATION ANTIBODY 4C6 FAB AT PH 4.6 WITH A DATA SET COLLECTED AT SSRL BEAMLINE 9-1
1rul CRYSTAL STRUCTURE OF U.V.-IRRADIATED CATIONIC CYCLIZATION ANTIBODY 4C6 FAB AT PH 5.6 WITH A DATA SET COLLECTED AT SSRL BEAMLINE 11-1.
1rum CRYSTAL STRUCTURE OF H2O2-SOAKED CATIONIC CYCLIZATION ANTIBODY 4C6 FAB AT PH 8.5 WITH A DATA SET COLLECTED AT SSRL BEAMLINE 9-1.
1rup CRYSTAL STRUCTURE OF NATIVE CATIONIC CYCLIZATION ANTIBODY 4C6 FAB AT PH 8.5 WITH A DATA SET COLLECTED AT APS BEAMLINE 19-ID