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(-) Description

Title :  CRYSTAL STRUCTURE OF MONOCLONAL ANTI-HUMAN PODOPLANIN ANTIBODY NZ-1 WITH BOUND PA PEPTIDE
 
Authors :  Y. Fujii, Y. Kitago, T. Arimori, J. Takagi
Date :  11 Mar 15  (Deposition) - 02 Mar 16  (Release) - 13 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.56
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E  (1x)
Biol. Unit 2:  C,D,F  (1x)
Keywords :  Antibodies, Monoclonal, Antibody Affinity, Chromatography, Affinity, Epitopes, Rats, Immunoglobulin Fab Fragments, Kinetics, Peptides, Protein Binding, Proteins, Recombinant Fusion Proteins, Human Podoplanin, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Fujii, Y. Matsunaga, T. Arimori, Y. Kitago, S. Ogasawara, M. K. Kaneko, Y. Kato, J. Takagi
Tailored Placement Of A Turn-Forming Pa Tag Into The Structured Domain Of A Protein To Probe Its Conformational State
J. Cell. Sci. V. 129 1512 2016
PubMed-ID: 26872787  |  Reference-DOI: 10.1242/JCS.176685

(-) Compounds

Molecule 1 - HEAVY CHAIN OF ANTIGEN BINDING FRAGMENT, FAB
    ChainsA, C
    EngineeredYES
    Expression SystemMUS MUSCULUS
    Expression System Taxid10090
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
 
Molecule 2 - LIGHT CHAIN OF ANTIGEN BINDING FRAGMENT, FAB
    ChainsB, D
    EngineeredYES
    Expression SystemMUS MUSCULUS
    Expression System Taxid10090
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
 
Molecule 3 - PA14 PEPTIDE
    ChainsE, F
    EngineeredYES
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)AB  E 
Biological Unit 2 (1x)  CD F

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2PCA2Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY C:63 , ASN D:27 , GLY D:121 , HOH D:422 , HOH D:445 , HOH D:470binding site for residue EDO D 301
2AC2SOFTWAREVAL D:22 , ARG D:43 , THR D:45 , TYR D:113 , SER D:114 , SER D:115 , GLY D:116 , VAL D:118 , HOH D:410 , HOH D:439binding site for Di-peptide PCA D 20 and PHE D 21

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:41 -A:115
2A:163 -A:218
3B:41 -B:110
4B:156 -B:214
5C:41 -C:115
6C:163 -C:218
7D:41 -D:110
8D:156 -D:214

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Phe A:169 -Pro A:170
2Glu A:171 -Pro A:172
3Tyr B:162 -Pro B:163
4Phe C:169 -Pro C:170
5Glu C:171 -Pro C:172
6Tyr D:162 -Pro D:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YO0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YO0)

(-) Exons   (0, 0)

(no "Exon" information available for 4YO0)

(-) Sequences/Alignments

Asymmetric 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:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee....eeee...eeeee........eeeee...eeeeeeeeeee.....eeee........eee...eee..eeeeeeeeeeehhhhh....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yo0 A  20 EVQLVESGGGLVQPGRSLKLSCAASGFTFSNYGMAWVRQTPTKGLEWIASISAGGDKTYYGDSVKGRFSISRDNAKTTHYLQMDSLRSEDTATYYCAKTSRVYFDYWGQGVMVTVSSAETTAPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGALSSGVHTFPAVLQSGLYTLTSSVTVPSSTWSSQAVTCNVAHPASSTKVDKKIVP 235
                                    29        39        49        59        69        79        89        99       109       119       129       139       149|      166       176       186       196       206       216       226         
                                                                                                                                                           149|                                                                              
                                                                                                                                                            157                                                                              

Chain B from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee...eeeee....eeeeeee...hhhhh..eeeee......eeee.............eeeeeehhh.eeeeee...hhhhheeeeeeee...eee...eeeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eee...eee..eeeeeeeeeeehhhhhhh..eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yo0 B  20 xFVLTQPNSVSTNLGSTVKLSCKRSTGNIGSNYVNWYQQHEGRSPTTMIYRDDKRPDGVPDRFSGSIDRSSNSALLTINNVQTEDEADYFCHSYSSGIVFGGGTKLTVLGQPKSTPTLTVFPPSTEELQGNKATLVCLISDFYPSDVEVAWKANGAPISQGVDTANPTKQGNKYIASSFLRLTAEQWRSRNSFTCQVTHEGNTVEKSLSP 229
                            |       29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229
                           20-PCA                                                                                                                                                                                                             

Chain C from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee....eeee...eeeee........eeeee.....eeeeeeee.....eeee.hhh....eee...eee..eeeeeeee..eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yo0 C  20 EVQLVESGGGLVQPGRSLKLSCAASGFTFSNYGMAWVRQTPTKGLEWIASISAGGDKTYYGDSVKGRFSISRDNAKTTHYLQMDSLRSEDTATYYCAKTSRVYFDYWGQGVMVTVSSAETTAPSVYPLAPMVTLGCLVKGYFPEPVTVTWNSGALSSGVHTFPAVLQSGLYTLTSSVTVTCNVAHPASSTKVDKKIVP 235
                                    29        39        49        59        69        79        89        99       109       119       129       139       149|      167       177       187       197       217       227        
                                                                                                                                                           149|                                            205|                   
                                                                                                                                                            158                                             216                   

Chain D from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee...eeeee....eeeeeee...hhhhh..eeeee......eeee.............eeeeee....eeeeee...hhhhheeeeeeee...eee...eeeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eee...eee..eeeeeeeeeeehhhhhh...eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yo0 D  20 xFVLTQPNSVSTNLGSTVKLSCKRSTGNIGSNYVNWYQQHEGRSPTTMIYRDDKRPDGVPDRFSGSIDRSSNSALLTINNVQTEDEADYFCHSYSSGIVFGGGTKLTVLGQPKSTPTLTVFPPSTEELQGNKATLVCLISDFYPSDVEVAWKANGAPISQGVDTANPTKQGNKYIASSFLRLTAEQWRSRNSFTCQVTHEGNTVEKSLSP 229
                            |       29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229
                           20-PCA                                                                                                                                                                                                             

Chain E from PDB  Type:PROTEIN  Length:12
                                            
               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
                 4yo0 E   3 GVAMPGAEDDVV  14
                                    12  

Chain F from PDB  Type:PROTEIN  Length:11
                                           
               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
                 4yo0 F   4 VAMPGAEDDVV  14
                                    13 

   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 4YO0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YO0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YO0)

(-) Gene Ontology  (34, 34)

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4yny