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(-) Description

Title :  CRYSTAL STRUCTURE OF S25-26 IN COMPLEX WITH KDO(2.8)KDO(2.4)KDO TRISACCHARIDE
 
Authors :  O. Haji-Ghassemi, S. V. Evans, S. Muller-Loennies, R. Saldova, M. Muni L. Brade, P. M. Rudd, D. J. Harvey, P. Kosma, H. Brade
Date :  12 Aug 13  (Deposition) - 09 Apr 14  (Release) - 09 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Beta-Sandwich, Carbohydrate/Sugar Binding, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Haji-Ghassemi, S. Muller-Loennies, R. Saldova, M. Muniyappa, L. Brade, P. M. Rudd, D. J. Harvey, P. Kosma, H. Brade, S. V. Evans
Groove-Type Recognition Of Chlamydiaceae-Specific Lipopolysaccharide Antigen By A Family Of Antibodies Possessing An Unusual Variable Heavy Chain N-Linked Glycan.
J. Biol. Chem. V. 289 16644 2014
PubMed-ID: 24682362  |  Reference-DOI: 10.1074/JBC.M113.528224

(-) Compounds

Molecule 1 - S25-26 FAB (IGG1K) HEAVY CHAIN
    Chains: H
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 2 - S25-26 FAB (IGG1K) LIGHT CHAIN
    Chains: L
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric/Biological Unit (5, 6)
No.NameCountTypeFull Name
1K1Ligand/IonPOTASSIUM ION
2KDA1Ligand/Ion(3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID)-2-O-ALLYL
3KDO2Ligand/Ion3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR H:30 , THR H:31 , THR H:117 , PRO H:118 , GLY H:144 , HOH H:514BINDING SITE FOR RESIDUE K H 302
2AC2SOFTWARETYR L:27ABINDING SITE FOR RESIDUE PEG L 301
3AC3SOFTWARELYS H:43 , ASN H:85 , HOH H:534BINDING SITE FOR MONO-SACCHARIDE NAG H 301 BOUND TO ASN H 85
4AC4SOFTWARETHR H:31 , GLY H:33 , TRP H:52 , SER H:53 , GLY H:54 , GLY H:55 , SER H:56 , ARG H:94 , ARG H:96 , THR H:98 , LYS H:115 , THR H:116 , SER H:202 , HOH H:404 , HOH H:410 , HOH H:423 , HOH H:426 , HOH H:440 , HOH H:442 , HOH H:443 , HOH H:447 , HOH H:453 , HOH H:457 , HOH H:458 , HOH H:483 , HOH H:501 , HIS L:27D , ASN L:28 , TYR L:32 , TYR L:96 , LYS L:147 , GLU L:154 , GLN L:156 , HOH L:435BINDING SITE FOR CHAIN H OF POLYSACCHARIDE RESIDUES 303 TO 305

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:140 -H:195
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ala H:129 -Ala H:130
2Ser H:134 -Met H:135
3Phe H:146 -Pro H:147
4Glu H:148 -Pro H:149
5Trp H:188 -Pro H:189
6Thr L:7 -Pro L:8
7Val L:94 -Pro L:95
8Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M7J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M7J)

(-) Exons   (0, 0)

(no "Exon" information available for 4M7J)

(-) 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:219
                                                                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeee...eeeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeee...............eeeee........eeeee...........eeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeee..........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m7j H    1 EVQLKESGPGLVQPSQSLSITCTVSGFSLTTYGVHWVRQSPGKGLEWLGVIWSGGSTDYNAAFISRLSISKDNSKSHVFFKMNSLQANDTAIYYCARMRITTDWFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD  214
                                    10        20        30        40        50        60        70        80  |||   87        97   ||  105       115       125       135       145       155       165       175       185       195       205         
                                                                                                            82A||               100A|                                                                                                                  
                                                                                                             82B|                100B                                                                                                                  
                                                                                                              82C                                                                                                                                      


Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d4m7jl1 L:1-107 automated matches                                                                               d4m7jl2 L:108-214 automated matches                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m7j L    1 DILMNQTPLSLPVSLGDQASISCRSSQYIVHRNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    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
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  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 4M7J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M7J)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4M7J)

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  Cis Peptide Bonds
    Ala H:129 - Ala H:130   [ RasMol ]  
    Glu H:148 - Pro H:149   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Ser H:134 - Met H:135   [ RasMol ]  
    Thr L:7 - Pro L:8   [ RasMol ]  
    Trp H:188 - Pro H:189   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
    Val L:94 - Pro L:95   [ RasMol ]  
 

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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

4m7z SAME PROTEIN, UNLIGANDED STRUCTURE 1
4m93 SAME PROTEIN, UNLIGANDED STRUCTURE 2
4ma1 SAME PROTEIN, UNLIGANDED STRUCTURE 3