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(-) Description

Title :  CRYSTAL STRUCTURE OF SCFV-SM3 IN COMPLEX WITH APD-SGALNAC-RP
 
Authors :  N. Martinez-Saez, J. Castro-Lopez, J. Valero-Gonzalez, D. Madariaga I. Companon, V. J. Somovilla, M. Salvado, J. L. Asensio, J. Jimenez-Ba A. Avenoza, J. H. Busto, G. J. L. Bernardes, J. M. Peregrina, R. Hurtado-Guerrero, F. Corzana
Date :  20 May 15  (Deposition) - 03 Jun 15  (Release) - 26 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym./Biol. Unit :  H,P
Keywords :  Immune System, Glycopeptides, Antibodies, Molecular Recognition, Conformation Analysis, Fusion Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Martinez-Saez, J. Castro-Lopez, J. Valero-Gonzalez, D. Madariaga, I. Companon, V. J. Somovilla, M. Salvado, J. L. Asensio, J. Jimenez-Barbero, A. Avenoza, J. H. Busto, G. J. L. Bernardes, J. M. Peregrina, R. Hurtado-Guerrero, F. Corzana
Deciphering The Non-Equivalence Of Serine And Threonine O- Glycosylation Points: Implications For Molecular Recognition Of The Tn Antigen By An Anti-Muc1 Antibody.
Angew. Chem. Int. Ed. Engl. V. 54 9830 2015
PubMed-ID: 26118689  |  Reference-DOI: 10.1002/ANIE.201502813

(-) Compounds

Molecule 1 - IG LAMBDA-1 CHAIN V REGION S43
    Chains: H
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Plasmid: PPICZALPHAA
    Expression System Strain: X33
    Expression System Taxid: 4922
    Fragment: RESIDUES 6-115,20-129
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: SCFV-SM3
 
Molecule 2 - ANTIGEN TN, SER IS COVALENTLY BOUND TO GALNAC
    Chains: P
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN H:31 , LEU H:52A , ARG P:5BINDING SITE FOR RESIDUE EDO H3113
2AC2SOFTWARESER H:1009BINDING SITE FOR RESIDUE EDO H3108
3AC3SOFTWAREALA P:1 , PRO P:2 , ASP P:3 , SER P:4 , ARG P:5BINDING SITE FOR MONO-SACCHARIDE A2G P1009 BOUND TO SER P 4

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:1023 -H:1088

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly H:96 -Gln H:97
2Pro H:1040 -Asp H:1041

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A2I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A2I)

(-) Exons   (0, 0)

(no "Exon" information available for 5A2I)

(-) 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:224
                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeee.......eeeeee.hhhhh..eee.......eeeeeehhh.eeeeee...hhhhheeeeeee.....ee...eeeee..eee..eeee....eeeeeeee.....hhhhh.eeeeee...eeeeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeeee....eee...eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
               5a2i H     1 QVQLQESGGGLVQPGGSMKLSCVASGFTFSNYWMNWVRQSPEKGLEWVAEIRLKSNNYATHYAESVKGRFTISRDDSKSSVYLQMNNLRAEDTGIYYCTGVGQFAYWGQGTTVTVSVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLG  1107
                                    10        20        30        40        50  |||   57        67        77     |||84        94   ||  106     |1007      1017      1027|||   1034      1044      1054      1064      1074      1084      1094      1104  | 
                                                                              52A||                            82A||              98|        112|                   1027A||                                                                           1106A 
                                                                               52B|                             82B|              101        1004                    1027B|                                                                                 
                                                                                52C                              82C                                                  1027C                                                                                 


Chain P from PDB  Type:PROTEIN  Length:6
                                        
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
               5a2i P     1 APDSRP     6
   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  (0, 0)

(no "SCOP Domain" information available for 5A2I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A2I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A2I)

(-) Gene Ontology  (1, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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    Gly H:96 - Gln H:97   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        HVM32_MOUSE | P01801: 1m71 1m7d 1m7i 1pz5 1sm3 2dlf 5a2j 5a2k 5a2l
        LV1E_MOUSE | P01727: 5a2j 5a2k 5a2l

(-) Related Entries Specified in the PDB File

5a2j CRYSTAL STRUCTURE OF SCFV-SM3 IN COMPLEX WITH THE NAKED PEPTIDE APDTRP
5a2k CRYSTAL STRUCTURE OF SCFV-SM3 IN COMPLEX WITH APD- TGALNAC-RP
5a2l CRYSTAL STRUCTURE OF SCFV-SM3 IN COMPLEX WITH APD- CGALNAC-RP