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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF KKO
 
Authors :  Z. Cai, Z. Zhu, Q. Liu, M. I. Greene
Date :  03 Sep 14  (Deposition) - 16 Dec 15  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  B,C
Keywords :  Immunoglobulin, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Cai, S. V. Yarovoi, Z. Zhu, L. Rauova, V. Hayes, T. Lebedeva, Q. Liu, M. Poncz, G. Arepally, D. B. Cines, M. I. Greene
Atomic Description Of The Immune Complex Involved In Heparin-Induced Thrombocytopenia.
Nat Commun V. 6 8277 2015
PubMed-ID: 26391892  |  Reference-DOI: 10.1038/NCOMMS9277

(-) Compounds

Molecule 1 - PLATELET FACTOR 4 ANTIBODY KKO LIGHT CHAIN
    Chains: B
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell: HYBRIDOMA
    Expression System Taxid: 10090
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - PLATELET FACTOR 4 ANTIBODY KKO HEAVY CHAIN
    Chains: C
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell: HYBRIDOMA
    Expression System Taxid: 10090
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : BC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2ZN2Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:151 , HIS B:189 , GLU C:61 , GLU C:64BINDING SITE FOR RESIDUE ZN B 301
2AC2SOFTWARELYS B:24 , THR B:69 , ASP B:70 , ASP C:213BINDING SITE FOR RESIDUE GOL B 302
3AC3SOFTWARELYS B:142 , ASP B:143BINDING SITE FOR RESIDUE GOL B 303
4AC4SOFTWAREASN B:157 , PHE C:32 , GLU C:49 , HOH C:401BINDING SITE FOR RESIDUE GOL B 304
5AC5SOFTWAREPRO B:40 , ASP B:165 , HOH B:405BINDING SITE FOR RESIDUE GOL B 305
6AC6SOFTWAREASP B:167 , HOH B:431 , HOH B:432 , HIS C:170BINDING SITE FOR RESIDUE ZN C 301
7AC7SOFTWAREGLN B:42 , TYR C:94 , GLN C:111BINDING SITE FOR RESIDUE GOL C 302

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1B:23 -B:88
2B:134 -B:194
3B:214 -C:134
4C:21 -C:95
5C:146 -C:201

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr B:94 -Pro B:95
2Tyr B:140 -Pro B:141
3Phe C:152 -Pro C:153
4Glu C:154 -Ser C:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R97)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R97)

(-) Exons   (0, 0)

(no "Exon" information available for 4R97)

(-) 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 B from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r97 B   1 DIQMIQSQKFMSTSVGDRVTVTCKASQNVGTNVAWYQQKPGQSPNALIYSASYRYSGVPDRFTGSGSGTDFTLTITNVQSEDLADYFCQQYNSYPLTFGTGTKLDLKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    


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.....eeeeeee...hhh.eeeeeeee.....eeeeeee......eeehhhhhh.eeeeee....eeeeee...hhhhheeeeeeeee........ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r97 C   1 VQLQQSGAELVKPGASVKLSCKASGYTFTNYFIYWVKQRPGQGLEWIGEINPRNGDTDFNEKFESRATLTVDKSSSTAYMQLSSLTSEDSAIYYCTRSPYGNNYGFTYWGQGTLVTVSAAKTTPPSVYPLAPGCGDAAGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEP 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 4R97)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R97)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R97)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4R97)

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  Cis Peptide Bonds
    Glu C:154 - Ser C:155   [ RasMol ]  
    Phe C:152 - Pro C:153   [ RasMol ]  
    Tyr B:140 - Pro B:141   [ RasMol ]  
    Tyr B:94 - Pro B:95   [ RasMol ]  
 

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  4r97
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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4R97)

(-) Related Entries Specified in the PDB File

4r9w PLATELET FACTOR 4
4r9y KKOFAB IN COMPLEX WITH PLATELET FACTOR 4