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(-) Description

Title :  STRUCTURE OF AN ANTI-METHOTREXATE CDR1-3 GRAFT VHH ANTIBODY IN COMPLEX WITH METHOTREXATE
 
Authors :  S. W. Fanning, J. R. Horn
Date :  02 Mar 11  (Deposition) - 06 Jul 11  (Release) - 11 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Camelid Single Domain Antibody, Heavy Chain Only, Vhh, Antibody, Anti-Hapten Antibody, Cdr, Hapten Binding, Small Molecule Sensing, Ligand Binding, Low Molecular Weight Compound, Methotrexate, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. W. Fanning, J. R. Horn
An Anti-Hapten Camelid Antibody Reveals A Cryptic Binding Site With Significant Energetic Contributions From A Nonhypervariable Loop.
Protein Sci. V. 20 1196 2011
PubMed-ID: 21557375  |  Reference-DOI: 10.1002/PRO.648

(-) Compounds

Molecule 1 - ANTI-METHOTREXATE CDR1-3 GRAFT VHH
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: LLAMA
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1MTX2Ligand/IonMETHOTREXATE
2NA5Ligand/IonSODIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MTX1Ligand/IonMETHOTREXATE
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MTX1Ligand/IonMETHOTREXATE
2NA-1Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:4 , CYS A:24 , ALA A:26 , ARG A:28 , ARG A:29 , SER A:30 , SER A:31 , ARG A:32 , TRP A:34 , ARG A:74 , ASP A:75 , ASN A:79 , THR A:80 , VAL A:81 , ALA A:100 , HOH A:1005 , HOH A:1064 , HOH A:1118 , ARG B:58BINDING SITE FOR RESIDUE MTX A 2000
2AC2SOFTWAREARG A:74 , HOH A:1023 , HOH A:1026 , HOH A:1098 , HOH A:1106 , HOH A:1120BINDING SITE FOR RESIDUE NA A 132
3AC3SOFTWAREASP A:101 , ASP A:102 , GLY A:112 , ASP A:119 , HOH A:1018 , HOH A:1066BINDING SITE FOR RESIDUE NA A 133
4AC4SOFTWAREVAL B:4 , CYS B:24 , ALA B:26 , ARG B:28 , ARG B:29 , SER B:30 , SER B:31 , ARG B:32 , TRP B:34 , MET B:36 , ARG B:74 , ASP B:75 , ASN B:79 , THR B:80 , VAL B:81 , ALA B:100 , HOH B:1022BINDING SITE FOR RESIDUE MTX B 2000
5AC5SOFTWAREASP B:101 , ASP B:102 , GLY B:112 , ASP B:119 , NA B:133 , HOH B:1044 , HOH B:1087BINDING SITE FOR RESIDUE NA B 132
6AC6SOFTWARESER B:111 , GLY B:112 , NA B:132 , HOH B:1017 , HOH B:1044 , HOH B:1055 , HOH B:1083BINDING SITE FOR RESIDUE NA B 133
7AC7SOFTWAREARG B:74 , HOH B:1018 , HOH B:1034 , HOH B:1048 , HOH B:1075BINDING SITE FOR RESIDUE NA B 134

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:24 -A:98
2B:24 -B:98

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QXT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains d3qxta_ A: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee....eeeeeee........eeeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee...hhhhh.....ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qxt A   3 QVQLVESGGGLVQAGGSLRLSCAASRRSSRSWAMAWFRQAPGKEREFVAKISGDGRLTTYGDSVKGRFTISRDKGKNTVYLQMDSLKPEDTAVYYCAADDNYVTASWRSGPDYWGQGTQVTVSS 131
                                    12        22        32        42        52        62        72        82        92       102       112||     127    
                                                                                                                                        113|            
                                                                                                                                         119            


Chain B from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains d3qxtb_ B: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee....eeeeeee........eeeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee..hhhhhh.....ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qxt B   3 QVQLVESGGGLVQAGGSLRLSCAASRRSSRSWAMAWFRQAPGKEREFVAKISGDGRLTTYGDSVKGRFTISRDKGKNTVYLQMDSLKPEDTAVYYCAADDNYVTASWRSGPDYWGQGTQVTVSS 131
                                    12        22        32        42        52        62        72        82        92       102       112||     127    
                                                                                                                                        113|            
                                                                                                                                         119
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 Classification and Annotation

(-) SCOP Domains  (1, 2)

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

(-) CATH Domains  (0, 0)

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

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(-) Gene Ontology  (0, 0)

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 Related Entries

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(-) Related Entries Specified in the PDB File

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