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(-) Description

Title :  TGFALPHA/EPIREGULIN COMPLEX WITH NEUTRALIZING ANTIBODY LY3016859
 
Authors :  S. Atwell, J. S. Boyles, D. K. Clawson, Z. Druzina, G. H. Josef, K. Weiche D. R. Witcher
Date :  27 Jun 16  (Deposition) - 31 Aug 16  (Release) - 02 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Tgfalpha Epiregulin Antibody Fab, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Boyles, S. Atwell, Z. Druzina, J. G. Heuer, D. R. Witcher
Structural Basis Of Selectivity And Neutralizing Activity O A Tgf Alpha /Epiregulin Specific Antibody.
Protein Sci. V. 25 2028 2016
PubMed-ID: 27543934  |  Reference-DOI: 10.1002/PRO.3023

(-) Compounds

Molecule 1 - EPIREGULIN ANTIBODY LY3016859 FAB HEAVY CHAIN
    Chains: A, D
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Taxid: 10029
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - EPIREGULIN ANTIBODY LY3016859 FAB LIGHT CHAIN
    Chains: B, E
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Taxid: 10029
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - PROTRANSFORMING GROWTH FACTOR ALPHA
    Chains: C, F
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:1 , VAL A:2 , TYR A:107 , HOH A:426 , GLN D:1 , VAL D:2 , TYR D:107binding site for residue SO4 A 301
2AC2SOFTWAREHIS C:18 , HIS C:35 , HIS F:18 , HIS F:35binding site for residue ZN C 101

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:22 -A:96
2A:145 -A:201
3B:23 -B:93
4B:139 -B:199
5C:16 -C:32
6C:34 -C:43
7D:22 -D:96
8D:145 -D:201
9E:23 -E:93
10E:139 -E:199
11F:16 -F:32
12F:34 -F:43

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Phe A:151 -Pro A:152
2Val B:99 -Pro B:100
3Tyr B:145 -Pro B:146
4Phe D:151 -Pro D:152
5Glu D:153 -Pro D:154
6Ser E:7 -Pro E:8
7Val E:99 -Pro E:100
8Tyr E:145 -Pro E:146
9Ser F:11 -His F:12

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KN5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KN5)

(-) Exons   (0, 0)

(no "Exon" information available for 5KN5)

(-) 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:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee......eeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.......ee...eeeee........eeeee.......eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhhhh..eeeeeeehhhheeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kn5 A   1 QVQLVQSGAEVKKPGSSVKVSCKASGYTFTDAYINWVRQAPGQGLEWMGWIWPGPVITYYNPKFKGRVTITADKSTSTAYMELSSLRSEDTAVYYCARREVLSPFAYWGQGTTVTVSSASTKGPSVFPLAPCSSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVE 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  ||   143       153       163       173       183       193       203       213    
                                                                                                                                                              133|                                                                                
                                                                                                                                                               137                                                                                


Chain B from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee...eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5kn5 B   1 DIVMTQSPDSLAVSLGERATINCRSSQSIVHSTGNTYLEWYQQKPGQPPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCFHGTHVPYTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 216
                                    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:40
                                                                        
               SCOP domains ---------------------------------------- SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee....eeeeee...ee.....ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                 5kn5 C  10 DSHTQFCFHGTCRFLVQEDKPACVCHSGYVGARCEHADLL  49
                                    19        29        39        49


Chain D from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee......eeeeeee....eeee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee.......ee...eeeee........eeeee........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhh...eeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kn5 D   1 QVQLVQSGAEVKKPGSSVKVSCKASGYTFTDAYINWVRQAPGQGLEWMGWIWPGPVITYYNPKFKGRVTITADKSTSTAYMELSSLRSEDTAVYYCARREVLSPFAYWGQGTTVTVSSASTKGPSVFPLAPCSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVE 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 ||    142       152       162       172       182       192       202       212     
                                                                                                                                                             132|                                                                                  
                                                                                                                                                              135                                                                                  


Chain E from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee......eee.........eeeeeeeeeehhhhhh..eeeeeee.......ee..ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5kn5 E   1 DIVMTQSPDSLAVSLGERATINCRSSQSIVHSTGNTYLEWYQQKPGQPPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCFHGTHVPYTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      


Chain F from PDB  Type:PROTEIN  Length:39
                                                                       
               SCOP domains --------------------------------------- SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee....eeeeee...ee.....ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
                 Transcript --------------------------------------- Transcript
                 5kn5 F  11 SHTQFCFHGTCRFLVQEDKPACVCHSGYVGARCEHADLL  49
                                    20        30        40
   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 5KN5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KN5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KN5)

(-) Gene Ontology  (25, 25)

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 Related Entries

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UniProtKB/Swiss-Prot
        TGFA_HUMAN | P01135: 1gk5 1mox 1p9j 1yuf 1yug 2tgf 3e50 3tgf 4tgf

(-) Related Entries Specified in the PDB File

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