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(-) Description

Title :  CRYSTAL STRUCTURE OF S25-39 IN COMPLEX WITH KDO(2.4)KDO
 
Authors :  R. J. Blackler, S. V. Evans
Date :  25 Aug 10  (Deposition) - 06 Apr 11  (Release) - 04 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Antibody, Fab, Igg, Carbohydrate, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. J. Blackler, C. L. Brooks, D. W. Evans, L. Brade, P. Kosma, H. Brade, S. V. Evans
A Common Nh53K Mutation In The Combining Site Of Antibodies Raised Against Chlamydial Lps Glycoconjugates Significantly Increases Avidity.
Biochemistry V. 50 3357 2011
PubMed-ID: 21405106  |  Reference-DOI: 10.1021/BI101886V

(-) Compounds

Molecule 1 - S25-39 FAB (IGG1K) LIGHT CHAIN
    Chains: A
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: ASCITES
    Strain: BALB/C
 
Molecule 2 - S25-39 FAB (IGG1K) HEAVY CHAIN
    Chains: B
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: ASCITES
    Strain: BALB/C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1KDA1Ligand/Ion(3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID)-2-O-ALLYL
2KDO1Ligand/Ion3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
3UNK1Mod. Amino Acid
4ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:138 , HIS B:173BINDING SITE FOR RESIDUE ZN A 216
2AC2SOFTWAREGLU A:185 , HIS A:189 , GLU B:61 , HOH B:328BINDING SITE FOR RESIDUE ZN B 223
3AC3SOFTWARETHR A:182 , TYR B:33 , LYS B:56 , KDO B:225 , HOH B:257 , HOH B:299 , HOH B:371BINDING SITE FOR RESIDUE KDA B 224
4AC4SOFTWAREASN A:27D , TYR A:32 , SER A:91 , TYR A:92 , ARG A:96 , ARG A:188 , HOH A:222 , TYR B:33 , ARG B:52 , HIS B:102 , GLU B:107A , KDA B:224 , HOH B:238 , HOH B:286 , HOH B:394BINDING SITE FOR RESIDUE KDO B 225

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3B:22 -B:98
4B:149 -B:204

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser A:7 -Pro A:8
2Tyr A:140 -Pro A:141
3Phe B:155 -Pro B:156
4Glu B:157 -Pro B:158
5Trp B:197 -Pro B:198

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OKK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OKK)

(-) Exons   (0, 0)

(no "Exon" information available for 3OKK)

(-) 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 A from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                             
               SCOP domains d3okka1 A:1-107 automated matches                                                                               d3okka2 A:108-215 automated matches                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.hhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3okk A    1 DIVMTQSPSSLAVSAGEKVTMNCKSSQSLLNSRTRKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFALTISSVQAEDLAVYYCKQSYNLRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERANGVLNSWTDQDSKDSTYSMTSTLTLTKDEYERHNSYTCEASHKTSTSPIVKSFNRNECx  215
                                    10        20       27C|||     34        44        54        64        74        84        94|      105       115       125       135       145       155       165       175       185       195       205       215
                                                     27A|||||                                                                 94|                                                                                                                    215-UNK
                                                      27B||||                                                                  96                                                                                                                       
                                                       27C|||                                                                                                                                                                                           
                                                        27D||                                                                                                                                                                                           
                                                         27E|                                                                                                                                                                                           
                                                          27F                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee......eeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeee..........ee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3okk B    1 EVKLVESGGGLVQPGGSLRLACATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKAKGYTTEYSASVKGRFTISRDNSQSSLYLQMNTLRAEDSATYYCARDHDGYYERFAYWGQGTLVTVSAAATTPPSVYPLAPGNSMVTLGCLVKGYFPEPVTVTWNSGSLSTGVHTFPAVLSSDLYTLTSSVTVPSKTWPSETVTCNVAHPASSTKVDKKIVPR  222
                                    10        20        30        40        50  |||   60        70        80     |||90       100      |110       120       130     ||145       155       165       175       185       195       205       215       
                                                                              53A||                            86A||               107A||                        136|                                                                                
                                                                               54B|                             87B|                108B|                         142                                                                                
                                                                                55C                              88C                 109C
   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  (2, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OKK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3OKK)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3OKK)

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

3mhl 3mhm 3mhn 3mho 3okd 3oke