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(-) Description

Title :  RECOGNITION OF THE THOMSEN-FRIEDENREICH ANTIGEN BY A LAMPREY VARIABLE LYMPHOCYTE RECEPTOR
 
Authors :  M. Luo, C. A. Velikovsky, X. B. Yang, R. A. Mariuzza
Date :  16 Apr 13  (Deposition) - 26 Jun 13  (Release) - 28 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Leucine Rich Repeat, Antigen Receptor, Thomsen-Friedenreich Antigen, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Luo, C. A. Velikovsky, X. Yang, M. A. Siddiqui, X. Hong, J. J. Barchi, J. C. Gildersleeve, Z. Pancer, R. A. Mariuzza
Recognition Of The Thomsen-Friedenreich Pancarcinoma Carbohydrate Antigen By A Lamprey Variable Lymphocyte Receptor.
J. Biol. Chem. V. 288 23597 2013
PubMed-ID: 23782692  |  Reference-DOI: 10.1074/JBC.M113.480467

(-) Compounds

Molecule 1 - VARIABLE LYMPHOCYTE RECEPTOR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7-7
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: MARINE LAMPREY
    Organism Scientific: PETROMYZON MARINUS
    Organism Taxid: 7757

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1A2G3Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2GAL3Ligand/IonBETA-D-GALACTOSE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:86 , GLY B:108 , CYS B:110 , GLY B:132 , ASP B:134 , TRP B:156 , A2G B:302 , HOH B:447BINDING SITE FOR RESIDUE GAL B 301
2AC2SOFTWARETRP B:62 , TRP B:84 , ASN B:86 , SER B:87 , GAL B:301BINDING SITE FOR RESIDUE A2G B 302
3AC3SOFTWARETRP C:84 , ASN C:86 , GLY C:108 , CYS C:110 , GLY C:132 , ASP C:134 , TRP C:156 , A2G C:302 , HOH C:422BINDING SITE FOR RESIDUE GAL C 301
4AC4SOFTWARETRP C:62 , TRP C:84 , ASN C:86 , SER C:87 , GAL C:301BINDING SITE FOR RESIDUE A2G C 302
5AC5SOFTWAREASN D:86 , GLY D:108 , CYS D:110 , GLY D:132 , ASP D:134 , TRP D:156 , A2G D:302 , HOH D:450 , HOH D:466BINDING SITE FOR RESIDUE GAL D 301
6AC6SOFTWAREHIS D:60 , TRP D:62 , TRP D:84 , ASN D:86 , SER D:87 , GAL D:301BINDING SITE FOR RESIDUE A2G D 302

(-) SS Bonds  (20, 20)

Asymmetric/Biological Unit
No.Residues
1A:3 -A:9
2A:7 -A:16
3A:110 -A:111
4A:164 -A:198
5A:166 -A:218
6B:3 -B:9
7B:7 -B:16
8B:110 -B:111
9B:164 -B:198
10B:166 -B:218
11C:3 -C:9
12C:7 -C:16
13C:110 -C:111
14C:164 -C:198
15C:166 -C:218
16D:3 -D:9
17D:7 -D:16
18D:110 -D:111
19D:164 -D:198
20D:166 -D:218

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Trp A:187 -Pro A:188
2Trp B:187 -Pro B:188
3Trp C:187 -Pro C:188
4Trp D:187 -Pro D:188

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K79)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K79)

(-) Exons   (0, 0)

(no "Exon" information available for 4K79)

(-) 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:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eee..................eee.....................eee.....................eee.....................eee.....................eee.....................eee.........hhhhhhhhhhhhhhhhh.ee....ee............hhhhh.....hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k79 A   2 ACPSQCSCSGTEVNCAGKSLASVPAGIPTTTRVLYLNSNQITKLEPGVFDRLANLRELHLWGNQLVSLPPGVFDNLANLEKLWLNSNQLTSLPAGLFDRLVNLEHLGLCCMKLTELPSGAFDKLTRLKQLGLDQNQLKSIPDGAFARLPSLTHVWLHTNPWDCQCTDILYLSGWVAQHSSIVGEGWPWRHSPDSAKCSGTNTPVRAVTEASTSPSKCP 219
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211        


Chain B from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eee..................eee.....................eee.....................eee.....................eee.....................eee.....................eee...........hhhhhhhhhhhh...eee....ee............hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k79 B   2 ACPSQCSCSGTEVNCAGKSLASVPAGIPTTTRVLYLNSNQITKLEPGVFDRLANLRELHLWGNQLVSLPPGVFDNLANLEKLWLNSNQLTSLPAGLFDRLVNLEHLGLCCMKLTELPSGAFDKLTRLKQLGLDQNQLKSIPDGAFARLPSLTHVWLHTNPWDCQCTDILYLSGWVAQHSSIVGEGWPWRHSPDSAKCSGTNTPVRAVTEASTSPSKCP 219
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211        


Chain C from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eee..................eee.....................eee.....................eee.....................eee.....................eee.....................eee.........hhhhhhhhhhhhhh...eee....ee............hhhhh.....hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k79 C   2 ACPSQCSCSGTEVNCAGKSLASVPAGIPTTTRVLYLNSNQITKLEPGVFDRLANLRELHLWGNQLVSLPPGVFDNLANLEKLWLNSNQLTSLPAGLFDRLVNLEHLGLCCMKLTELPSGAFDKLTRLKQLGLDQNQLKSIPDGAFARLPSLTHVWLHTNPWDCQCTDILYLSGWVAQHSSIVGEGWPWRHSPDSAKCSGTNTPVRAVTEASTSPSKCP 219
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211        


Chain D from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eee..................eee.....................eee.....................eee.....................eee.....................eee.....................eee.........hhhhhhhhhhhhhh...eee....ee............hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k79 D   2 ACPSQCSCSGTEVNCAGKSLASVPAGIPTTTRVLYLNSNQITKLEPGVFDRLANLRELHLWGNQLVSLPPGVFDNLANLEKLWLNSNQLTSLPAGLFDRLVNLEHLGLCCMKLTELPSGAFDKLTRLKQLGLDQNQLKSIPDGAFARLPSLTHVWLHTNPWDCQCTDILYLSGWVAQHSSIVGEGWPWRHSPDSAKCSGTNTPVRAVTEASTSPSKCP 219
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   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  (0, 0)

(no "SCOP Domain" information available for 4K79)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K79)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K79)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4K79)

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  4k79
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 Related Entries

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        K0IE77_PETMA | K0IE77: 4k5u

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4k5u