Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) 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
    Chains: A, C
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Taxid: 10090
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
 
Molecule 2 - LIGHT CHAIN OF ANTIGEN BINDING FRAGMENT, FAB
    Chains: B, D
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Taxid: 10090
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
 
Molecule 3 - PA14 PEPTIDE
    Chains: E, F
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 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)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PCA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:171 - Pro A:172   [ RasMol ]  
    Glu C:171 - Pro C:172   [ RasMol ]  
    Phe A:169 - Pro A:170   [ RasMol ]  
    Phe C:169 - Pro C:170   [ RasMol ]  
    Tyr B:162 - Pro B:163   [ RasMol ]  
    Tyr D:162 - Pro D:163   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4yo0
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PDPN_HUMAN | Q86YL7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PDPN_HUMAN | Q86YL7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PDPN_HUMAN | Q86YL7: 3wsr

(-) Related Entries Specified in the PDB File

4yny