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(-) Description

Title :  CRYSTAL STRUCTURE OF COMPLEMENT C5 IN COMPLEX WITH SKY59
 
Authors :  M. Irie, Y. Shimizu, Z. Sampei, T. Fukuzawa
Date :  03 Jun 16  (Deposition) - 03 May 17  (Release) - 03 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E  (1x)
Biol. Unit 2:  C,D,F  (1x)
Keywords :  Ph-Dependent, Recycling Antibody, Immune System, Complement C5, Fab, Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Fukuzawa, Z. Sampei, K. Haraya, Y. Ruike, M. Shida-Kawazoe, Y. Shimizu, S. W. Gan, M. Irie, Y. Tsuboi, H. Tai, T. Sakiyama, A. Sakamoto, S. Ishii, A. Maeda, Y. Iwayanagi, N. Shibahara, M. Shibuya, G. Nakamura, T. Nambu, A. Hayasaka, F. Mimoto, Y. Okura, Y. Hori, K. Habu, M. Wada, T. Miura, T. Tachibana, K. Honda, H. Tsunoda, T. Kitazawa, Y. Kawabe, T. Igawa, K. Hattori, J. Nezu
Long Lasting Neutralization Of C5 By Sky59, A Novel Recycling Antibody, Is A Potential Therapy For Complement-Mediated Diseases.
Sci Rep V. 7 1080 2017
PubMed-ID: 28439081  |  Reference-DOI: 10.1038/S41598-017-01087-7

(-) Compounds

Molecule 1 - SKY59 FAB LIGHT CHAIN
    ChainsA, C
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293F
    Expression System Taxid9606
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - SKY59 FAB HEAVY CHAIN
    ChainsB, D
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293F
    Expression System Taxid9606
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - COMPLEMENT C5 BETA CHAIN
    ChainsE, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    FragmentUNP RESIDUES 20-124
    GeneC5, CPAMD4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5B71)

(-) Sites  (0, 0)

(no "Site" information available for 5B71)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:137 -A:197
3B:22 -B:97
4B:150 -B:206
5C:23 -C:88
6C:137 -C:197
7D:22 -D:97
8D:150 -D:206

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Tyr A:143 -Pro A:144
3Phe B:156 -Pro B:157
4Glu B:158 -Pro B:159
5Ser C:7 -Pro C:8
6Tyr C:143 -Pro C:144
7Phe D:156 -Pro D:157
8Glu D:158 -Pro D:159
9Tyr E:59 -Pro E:60
10Tyr F:59 -Pro F:60

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5B71)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5B71)

(-) Exons   (0, 0)

(no "Exon" information available for 5B71)

(-) 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:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeee....eeeeee...hhhhh.eeeeee..............eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee......eeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b71 A   1 DIQMTQSPSSLSASVGDRVTITCRASQGISSSLAWYQQKPGKAPKLLIYGASETESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQNTKVGSSYGNTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       

Chain B from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..eee.....eeeeeeee........eeeeeee.....eeeeeeee.....eee.......eeeee.....eeeeee...hhhhheeeeeee.hhhhh......ee...eeeee........eeeee........eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhhhh...eeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5b71 B   2 VQLVESGGGLVQPGRSLRLSCAASGFTVHSSYYMAWVRQAPGKGLEWVGAIFTGSGAEYKAEWAKGRVTISKDTSKNQVVLTMTNMDPVDTATYYCASDAGYDYPTHAMHYWGQGTLVTVSSASTKGPSVFPLAPCSRSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESKY 225
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       143       153       163       173       183       193       203       213       223  
                                                                                                                                                                    140|                                                                                  
                                                                                                                                                                     143                                                                                  

Chain C from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeee.............eeeee...eeeeee...hhhhh.eeeeee..............eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b71 C   1 DIQMTQSPSSLSASVGDRVTITCRASQGISSSLAWYQQKPGKAPKLLIYGASETESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQNTKVGSSYGNTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    

Chain D from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eee.....eeeeeeee........eeeeeee.....eeeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeee............ee...eeeee........eeeee......eeeeeeeeee.....eeee........eee...ee.....eeeeeeeeehhhhhhh..eeeeeee....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b71 D   2 VQLVESGGGLVQPGRSLRLSCAASGFTVHSSYYMAWVRQAPGKGLEWVGAIFTGSGAEYKAEWAKGRVTISKDTSKNQVVLTMTNMDPVDTATYYCASDAGYDYPTHAMHYWGQGTLVTVSSASTKGPSVFPLAPCSRTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESKY 225
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       146       156       166       176       186       196       206       216         
                                                                                                                                                                   139|                                                                                
                                                                                                                                                                    145                                                                                

Chain E from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....ee...eeeeeeeee.....eeeeeeeee......eeeeeeeee......eeeeeee.....eeeeeee....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 5b71 E  20 EQTYVISAPKIFRVGASENIVIQVYGYTEAFDATISIKSYPDKKFSYSSGHVHLSSENKFQNSAILTIQPVSYVYLEVVSKHFSKSKRMPITY 121
                                    29        39        49        59        69        79        89|      108       118   
                                                                                                89|                      
                                                                                                 99                      

Chain F from PDB  Type:PROTEIN  Length:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....ee....eeeeeeee.....eeeeeeeee......eeeeeeeee......eeeeee......eeeeee....eeeeee.ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 5b71 F  20 EQTYVISAPKIFRVGASENIVIQVYGYTEAFDATISIKSYPDKKFSYSSGHVHLSSENKFQNSAILTIQPKYVYLEVVSKHFSKSKRMPITY 121
                                    29        39        49        59        69        79        89||     109       119  
                                                                                                 90|                    
                                                                                                 101                    

   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 5B71)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B71)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B71)

(-) Gene Ontology  (29, 29)

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  Cis Peptide Bonds
    Glu B:158 - Pro B:159   [ RasMol ]  
    Glu D:158 - Pro D:159   [ RasMol ]  
    Phe B:156 - Pro B:157   [ RasMol ]  
    Phe D:156 - Pro D:157   [ RasMol ]  
    Ser A:7 - Pro A:8   [ RasMol ]  
    Ser C:7 - Pro C:8   [ RasMol ]  
    Tyr A:143 - Pro A:144   [ RasMol ]  
    Tyr C:143 - Pro C:144   [ RasMol ]  
    Tyr E:59 - Pro E:60   [ RasMol ]  
    Tyr F:59 - Pro F:60   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        CO5_HUMAN | P010311cfa 1kjs 1xwe 3cu7 3hqa 3hqb 3kls 3km9 3prx 3pvm 4a5w 4e0s 4p39 4uu9 5b4p 5hcc 5hcd 5hce 5i5k

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5B71)