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(-) Description

Title :  DE NOVO DESIGN AND CRYSTALLOGRAPHIC VALIDATION OF ANTIBODIES TARGETING A PRE-SELECTED EPITOPE
 
Authors :  X. Liu, R. D. Taylor, L. Griffin, S. Coker, R. Adams, T. Ceska, J. Shi, A. D. G. Lawson, T. Baker
Date :  07 Dec 15  (Deposition) - 14 Dec 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  C,K,S,T
Biol. Unit 1:  K,S  (1x)
Biol. Unit 2:  C,T  (1x)
Keywords :  De Novo Protein, De Novo Design, Antibody Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Liu, S. Coker, T. Ceska, T. Baker
De Novo Design And Crystallographic Validation Of Antibodie Targeting A Pre-Selected Epitope
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - KELCH-LIKE ECH-ASSOCIATED PROTEIN 1
    Chains: K, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: KEAP1, INRF2, KIAA0132, KLHL19
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CYTOSOLIC INHIBITOR OF NRF2,INRF2,KELCH-LIKE PROTEIN 19
 
Molecule 2 - SINGLE CHAIN FV FROM A FAB
    Chains: T, S
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHO
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : CKST
Biological Unit 1 (1x):  KS 
Biological Unit 2 (1x): C  T

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5F72)

(-) Sites  (0, 0)

(no "Site" information available for 5F72)

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1S:22 -S:96
2S:44 -S:241
3S:164 -S:229
4T:22 -T:96
5T:44 -T:241
6T:164 -T:229

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser T:148 -Pro T:149
2Phe T:235 -Pro T:236
3Ser S:148 -Pro S:149
4Phe S:235 -Pro S:236

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F72)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F72)

(-) Exons   (0, 0)

(no "Exon" information available for 5F72)

(-) 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 C from PDB  Type:PROTEIN  Length:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........eeee........ee..........eeeee..eeeee..eeee..eeee...eeeee....eeee...........eeeee..eeeee..ee..ee...eeeee....eeeee..........eeeee..eeeeeeee....eeeeeeeee....eeee...........eeeee..eeeee...........eeeee....eeee...........eeeee..eeeee...........eeeee....eeeee..........eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f72 C 325 GRLIYTAGGYFRQSLSYLEAYNPSDGTWLDLADLQVPRSGLAGCVVGGLLYAVGGRNNSPDGNTDSSALDCYNPMTNQWSPCAPMSVPRNRIGVGVIDGHIYAVGGSHGCIHHNSVERYEPERDEWHLVAPMLTRRIGVGVAVLNRLLYAVGGFDGTNRLNSAECYYPERNEWRMITAMNTIRSGAGVCVLHNCIYAAGGYDGQDQLNSVERYDVETETWTFVAPMKHRRSALGITVHQGRIYVLGGYDGHTFLDSVECYDPDTDTWSEVTRMTSGRSGVGVAVT 609
                                   334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604     


Chain K from PDB  Type:PROTEIN  Length:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........eeee......eeee..........eeeee..eeeee..eeee..eeee...eeeee....eeee...........eeeee..eeeee..ee..ee...eeeee....eeeee..........eeeee..eeeee...........eeeee....eeeee..........eeeee..eeeee...........eeeee....eeeee..........eeeee..eeeee...........eeeee....eeeee..........eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f72 K 325 GRLIYTAGGYFRQSLSYLEAYNPSDGTWLDLADLQVPRSGLAGCVVGGLLYAVGGRNNSPDGNTDSSALDCYNPMTNQWSPCAPMSVPRNRIGVGVIDGHIYAVGGSHGCIHHNSVERYEPERDEWHLVAPMLTRRIGVGVAVLNRLLYAVGGFDGTNRLNSAECYYPERNEWRMITAMNTIRSGAGVCVLHNCIYAAGGYDGQDQLNSVERYDVETETWTFVAPMKHRRSALGITVHQGRIYVLGGYDGHTFLDSVECYDPDTDTWSEVTRMTSGRSGVGVAVT 609
                                   334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604     


Chain S from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eee.....eeeeeee........eeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeeeee..eeeeeee...eeeee......eeee..eee......eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f72 S   3 QLVESGGGLVQPGGSLRLSCAASGFAISASSIHWVRQAPGKCLEWVASIDPETGETLYAKSVAGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARAYAGDGVYYADVWGQGTLVTVSGSDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSYSFPSTFGCGTKVEI 247
                                    12        22        32        42        52        62        72        82        92       102       112       141       151       161       171       181       191       201       211       221       231       241      
                                                                                                                                               120|                                                                                                           
                                                                                                                                                140                                                                                                           


Chain T from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eee.....eeeeeee...hhhhheeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeeeee..eeeeeee...eeeee.......eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f72 T   3 QLVESGGGLVQPGGSLRLSCAASGFAISASSIHWVRQAPGKCLEWVASIDPETGETLYAKSVAGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARAYAGDGVYYADVWGQGTLVTVSSGSDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSYSFPSTFGCGTKVEIKR 249
                                    12        22        32        42        52        62        72        82        92       102       112       140       150       160       170       180       190       200       210       220       230       240         
                                                                                                                                                121|                                                                                                             
                                                                                                                                                 140
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 5F72)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F72)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F72)

(-) Gene Ontology  (35, 35)

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  Cis Peptide Bonds
    Phe S:235 - Pro S:236   [ RasMol ]  
    Phe T:235 - Pro T:236   [ RasMol ]  
    Ser S:148 - Pro S:149   [ RasMol ]  
    Ser T:148 - Pro T:149   [ RasMol ]  
 
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  5f72
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 Related Entries

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

UniProtKB/Swiss-Prot
        KEAP1_HUMAN | Q14145: 1u6d 1zgk 2flu 3vng 3vnh 3zgc 3zgd 4cxi 4cxj 4cxt 4ifj 4ifl 4ifn 4in4 4iqk 4l7b 4l7c 4l7d 4n1b 4xmb 5dad 5daf 5git 5nlb 5x54

(-) Related Entries Specified in the PDB File

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