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(-) Description

Title :  TNFALPHA-CERTOLIZUMAB FAB
 
Authors :  Y. S. Heo, J. U. Lee
Date :  21 Dec 16  (Deposition) - 07 Jun 17  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,L
Biol. Unit 1:  A,B,F  (1x)
Biol. Unit 2:  C,D,G  (1x)
Biol. Unit 3:  E,H,L  (1x)
Keywords :  Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. U. Lee, W. Shin, J. Y. Son, K. Y. Yoo, Y. S. Heo
Molecular Basis For The Neutralization Of Tumor Necrosis Factor Alpha By Certolizumab Pegol In The Treatment Of Inflammatory Autoimmune Diseases
Int J Mol Sci V. 18 2017
PubMed-ID: 28124979  |  Reference-DOI: 10.3390/IJMS18010228

(-) Compounds

Molecule 1 - HEAVY
    ChainsA, C, H
    EngineeredYES
    Expression SystemESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR PPPB1GAP_S
    Expression System Taxid1182034
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - LIGHT
    ChainsB, D, L
    EngineeredYES
    Expression SystemESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR PPPARG4
    Expression System Taxid1182032
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - TUMOR NECROSIS FACTOR ALPHA
    ChainsE, F, G
    EngineeredYES
    Expression SystemESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR PPPARG4
    Expression System Taxid1182032
    FragmentUNP RESIDUES 76-232
    GeneTNF
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  123456789
Asymmetric Unit ABCDEFGHL
Biological Unit 1 (1x)AB   F   
Biological Unit 2 (1x)  CD  G  
Biological Unit 3 (1x)    E  HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

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

(-) Sites  (0, 0)

(no "Site" information available for 5WUX)

(-) SS Bonds  (15, 15)

Asymmetric Unit
No.Residues
1A:22 -A:96
2A:145 -A:201
3B:23 -B:88
4B:134 -B:194
5C:22 -C:96
6C:145 -C:201
7D:23 -D:88
8D:134 -D:194
9E:69 -E:101
10F:69 -F:101
11G:69 -G:101
12H:22 -H:96
13H:145 -H:201
14L:23 -L:88
15L:134 -L:194

(-) Cis Peptide Bonds  (15, 15)

Asymmetric Unit
No.Residues
1Phe A:151 -Pro A:152
2Glu A:153 -Pro A:154
3Ser B:7 -Pro B:8
4Tyr B:94 -Pro B:95
5Tyr B:140 -Pro B:141
6Phe C:151 -Pro C:152
7Glu C:153 -Pro C:154
8Ser D:7 -Pro D:8
9Tyr D:94 -Pro D:95
10Tyr D:140 -Pro D:141
11Phe H:151 -Pro H:152
12Glu H:153 -Pro H:154
13Ser L:7 -Pro L:8
14Tyr L:94 -Pro L:95
15Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5WUX)

(-) 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:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee...eeeeeeeeee..hhhhheeeeeee.....eeeeeee......eee.......eeeeee....eeeeeeeeehhhhheeeeeeee.......ee...eeeee..........eee...eeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeee..........eeeee......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5wux A   1 EVQLVESGGGLVQPGGSLRLSCAASGYVFTDYGMNWVRQAPGKGLEWMGWINTYIGEPIYADSVKGRFTFSLDTSKSTAYLQMNSLRAEDTAVYYCARGYRSYAMDYWGQGTLVTVSSASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130||     148       158       168       178       188       198       208       218
                                                                                                                                                            131|                                                                              
                                                                                                                                                             140                                                                              

Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeee.hhh.....eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wux B   1 DIQMTQSPSSLSASVGDRVTITCKASQNVGTNVAWYQQKPGKAPKALIYSASFLYSGVPYRFSGSGSGTDFTLTISSLQPEDFATYYCQQYNIYPLTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 212
                                    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:202
                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee....eeeeeee....hhhhheeeeeee.....eeeeeee......eee.......eeeeee....eeeeeee..hhhhheeeeeeee.....eeee...eeeee........eeeee...eeeeeeee.....eeee........eee...ee.....eeeeeee.........eeee......eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wux C   1 EVQLVESGGGLVQPGGSLRLSCAASGYVFTDYGMNWVRQAPGKGLEWMGWINTYIGEPIYADSVKGRFTFSLDTSKSTAYLQMNSLRAEDTAVYYCARGYRSYAMDYWGQGTLVTVSSASTKGPSVFPLAPALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSTYICNVNHKPSNTKVDKKV 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130||     150       160       170       180       190  ||   204       214  
                                                                                                                                                            131|                                                193|                  
                                                                                                                                                             142                                                 198                  

Chain D from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee........eeeeeee......ee....eeeee......ee.......hhhhh..eeeeeeeeee............eeeee.........eeeeeeeeehhhhh.......eee........eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wux D   1 DIQMTQSPSSLSASVGDRVTITCKASQNVGTNVAWYQQKPGKAPKALIYSASFLYSGVPYRFSGSGSGTDFTLTISSLQPEDFATYYCQQYNIYPLTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVLQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKS 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     ||157       167       177       187       197       207 
                                                                                                                                                                           146|                                                      
                                                                                                                                                                            154                                                      

Chain E from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..............ee....eee..eee....eeeeeeeeeeeee.........eeeeeeee......eeeeeeeee......eeeeeeeeeeeee....eeeeee.hhhhh........eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wux E   9 SDKPVAHVVANPQAEGQLQWANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL 157
                                    18        28|       42        52        62        72        82        92       111       121       131       141       151      
                                              28|                                                                 101|                                              
                                               33                                                                  111                                              

Chain F from PDB  Type:PROTEIN  Length:141
                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.........ee......eee...eee..eee....eeeeeeeeeeeee.........eeeeeeeee....eeeeeeeeee.......eeeeeeeeeeeee....eeeeee.hhhhh........eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wux F   9 SDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL 157
                                    18        28        38        48        58        68        78        88        98   ||  116       126       136       146       156 
                                                                                                                       102|                                              
                                                                                                                        111                                              

Chain G from PDB  Type:PROTEIN  Length:141
                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.........ee......eee...eee..eee....eeeeeeeeeeeee.........eeeeeeee......eeeeeeeee.......eeeeeeeeeeeee....eeeeee.hhhhh........eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wux G   9 SDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL 157
                                    18        28        38        48        58        68        78        88        98   ||  116       126       136       146       156 
                                                                                                                       102|                                              
                                                                                                                        111                                              

Chain H from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.....eeee...eeeee........eeeee...eeeeeeeeee.....eeee........eee...ee.....eeeeeeeee..........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wux H   1 EVQLVESGGGLVQPGGSLRLSCAASGYVFTDYGMNWVRQAPGKGLEWMGWINTYIGEPIYADSVKGRFTFSLDTSKSTAYLQMNSLRAEDTAVYYCARGYRSYAMDYWGQGTLVTVSSASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130||     148       158       168       178       188       198       208       218  
                                                                                                                                                            131|                                                                                
                                                                                                                                                             140                                                                                

Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeee....eeeeee........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee....eeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wux L   1 DIQMTQSPSSLSASVGDRVTITCKASQNVGTNVAWYQQKPGKAPKALIYSASFLYSGVPYRFSGSGSGTDFTLTISSLQPEDFATYYCQQYNIYPLTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 213
                                    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 5WUX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu A:153 - Pro A:154   [ RasMol ]  
    Glu C:153 - Pro C:154   [ RasMol ]  
    Glu H:153 - Pro H:154   [ RasMol ]  
    Phe A:151 - Pro A:152   [ RasMol ]  
    Phe C:151 - Pro C:152   [ RasMol ]  
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    Tyr D:94 - Pro D:95   [ RasMol ]  
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5wuv