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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CD47 ECD BOUND TO FAB OF C47B222
 
Authors :  R. M. F. Cardoso
Date :  21 Nov 16  (Deposition) - 15 Mar 17  (Release) - 15 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  C,H,L
Keywords :  Antigen-Fab Complex, Immunoglobulin, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. C. Pietsch, J. Dong, R. Cardoso, X. Zhang, D. Chin, R. Hawkins, T. Dinh, M. Zhou, B. Strake, P. H. Feng, M. Rocca, C. D. Santos, X. Shan, G. Danet-Desnoyers, F. Shi, E. Kaiser, H. J. Millar, S. Fenton, R. Swanson, J. A. Nemeth, R. M. Attar
Anti-Leukemic Activity And Tolerability Of Anti-Human Cd47 Monoclonal Antibodies.
Blood Cancer J V. 7 E536 2017
PubMed-ID: 28234345  |  Reference-DOI: 10.1038/BCJ.2017.7

(-) Compounds

Molecule 1 - C47B222 FAB HEAVY CHAIN
    ChainsH
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293
    Expression System Taxid9606
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - C47B222 FAB LIGHT CHAIN
    ChainsL
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293
    Expression System Taxid9606
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - LEUKOCYTE SURFACE ANTIGEN CD47
    ChainsC
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293(GNTI-)
    Expression System Taxid9606
    FragmentEXTRACELLULAR DOMAIN, UNP RESIDUES 19-141
    GeneCD47, MER6
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymANTIGENIC SURFACE DETERMINANT PROTEIN OA3,INTEGRIN- ASSOCIATED PROTEIN,IAP,PROTEIN MER6

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit CHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE H:173 , PRO H:174 , SER H:184 , LEU H:185 , SER H:186 , GLN L:160 , SER L:162 , SER L:176 , THR L:178binding site for residue GOL L 301
2AC2SOFTWAREASN C:5binding site for Mono-Saccharide NAG C 201 bound to ASN C 5
3AC3SOFTWAREGLU C:11 , PHE C:12 , ASN C:16 , VAL C:19 , VAL C:20binding site for Mono-Saccharide NAG C 202 bound to ASN C 16
4AC4SOFTWAREASN C:32binding site for Mono-Saccharide NAG C 203 bound to ASN C 32
5AC5SOFTWAREASN C:55binding site for Poly-Saccharide residues NAG C 204 through NAG C 205 bound to ASN C 55
6AC6SOFTWAREASN C:93 , GLU C:110binding site for Poly-Saccharide residues NAG C 206 through NAG C 207 bound to ASN C 93

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1C:23 -C:96
2H:22 -H:96
3H:147 -H:203
4L:23 -L:88
5L:134 -L:194

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Phe H:153 -Pro H:154
2Glu H:155 -Pro H:156
3Ser L:7 -Pro L:8
4Trp L:94 -Pro L:95
5Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5TZ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TZ2)

(-) Exons   (0, 0)

(no "Exon" information available for 5TZ2)

(-) 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 C from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeee.....eeee..........hhh.eeeeeee...eeeeee....eee.hhhhh..ee.hhhhhhh...eeeehhhhh...eeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 5tz2 C   1 QLLFNKTKSVEFTFGNDTVVIPCFVTNMEAQNTTEVYVKWKFKGRDIYTFDGALNKSTVPTDFSSAKIEVSQLLKGDASLKMDKSDAVSHTGNYTCEVTELTREGETIIELKYR 114
                                    10        20        30        40        50        60        70        80        90       100       110    

Chain H from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee......eeeeee......eee........eeeee....eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee...eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tz2 H   1 EVQLVQSGAEVKKPGESLKISCKGSGYSFTDYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQGQVTISADKSISTAYLQWSSLKASDTAVYYCARVGRFASHQLDYWGQGTLVTVSSASTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  ||   147       157       167       177       187       197       207       217   
                                                                                                                                                              133|                                                                               
                                                                                                                                                               141                                                                               

Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tz2 L   1 EIVLTQSPATLSLSPGERATLSCRASQSVNNRLAWYQQKPGQAPRLLIHWASTRAIGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQGASWPFTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 212
                                    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 5TZ2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TZ2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TZ2)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  CD47_HUMAN | Q08722
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 Related Entries

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

UniProtKB/Swiss-Prot
        CD47_HUMAN | Q087222jjs 2jjt 2vsc 4cmm 4kjy 5iwl 5tzt 5tzu

(-) Related Entries Specified in the PDB File

5tzt 5tzu