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(-) Description

Title :  STRUCTURE OF LYMPHOTOXIN ALPHA BOUND TO ANTI-LTA FAB
 
Authors :  J. P. Yin, S. G. Hymowitz
Date :  26 Sep 13  (Deposition) - 13 Nov 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,D,E,F,H,L,X,Y
Keywords :  Tnf, Tumor Necrosis Factor, Tnfr Receptor, Lymphotoxin Beta Receptor, Lymphotoxin Alpha, Lymphoid Development, Tumor Immunity, Auto- Immunity, Cytokine-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Sudhamsu, J. Yin, E. Y. Chiang, M. A. Starovasnik, J. L. Grogan, S. G. Hymowitz
Dimerization Of Lt Beta R By Lt Alpha 1 Beta 2 Is Necessary And Sufficient For Signal Transduction.
Proc. Natl. Acad. Sci. Usa V. 110 19896 2013
PubMed-ID: 24248355  |  Reference-DOI: 10.1073/PNAS.1310838110

(-) Compounds

Molecule 1 - LYMPHOTOXIN-ALPHA
    Chains: A, B, D
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Gene: LTA, TNFB, TNFSF1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LT-ALPHA, TNF-BETA, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 1
 
Molecule 2 - ANTI-LYMPHOTOXIN ALPHA ANTIBODY LIGHT CHAIN
    Chains: E, L, X
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHO
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Fragment: FAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ANTI-LT-ALPHA ANTIBODY LIGHT CHAIN
 
Molecule 3 - ANTI-LYMPHOTOXIN ALPHA ANTIBODY HEAVY CHAIN
    Chains: F, H, Y
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHO
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Fragment: FAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ANTI-LT-ALPHA ANTIBODY HEAVY CHAIN

 Structural Features

(-) Chains, Units

  123456789
Asymmetric/Biological Unit : ABDEFHLXY

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4MXV)

(-) Sites  (0, 0)

(no "Site" information available for 4MXV)

(-) SS Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1E:23 -E:88
2E:134 -E:194
3F:22 -F:92
4F:140 -F:196
5H:22 -H:92
6H:140 -H:196
7L:23 -L:88
8L:134 -L:194
9X:23 -X:88
10X:134 -X:194
11Y:22 -Y:92

(-) Cis Peptide Bonds  (16, 16)

Asymmetric/Biological Unit
No.Residues
1Tyr A:108 -Pro A:109
2Ser E:7 -Pro E:8
3Thr E:94 -Pro E:95
4Tyr E:140 -Pro E:141
5Phe F:146 -Pro F:147
6Glu F:148 -Pro F:149
7Ser L:7 -Pro L:8
8Thr L:94 -Pro L:95
9Tyr L:140 -Pro L:141
10Phe H:146 -Pro H:147
11Glu H:148 -Pro H:149
12Ser X:7 -Pro X:8
13Thr X:94 -Pro X:95
14Tyr X:140 -Pro X:141
15Phe Y:146 -Pro Y:147
16Glu Y:148 -Pro Y:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MXV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MXV)

(-) Exons   (0, 0)

(no "Exon" information available for 4MXV)

(-) 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 A from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                          
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........ee......eee...eee..eee....eeeeeeeeeeeee......eeeeeeee......eeeeeeeee.........eeeeeeeeeeeee....eeeeeeehhhhh.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4mxv A   28 KPAAHLIGDPSKQNSLLWRANTDRAFLQDGFSLSNNSLLVPTSGIYFVYSQVVFSGKSSPLYLAHEVQLFSSQYPFHVPLLSSQKMVYPGLQEPWLHSMYHGAAFQLTQGDQLSTHTDGIPHLVLSPSTVFFGAFAL  171
                                    37        47        57        67        77      ||94       104       114       124       134       144       154       164       
                                                                                   84|                                                                               
                                                                                    92                                                                               


Chain B from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                          
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........ee......eee....ee..eee....eeeeeeeeeeeee....eeeeeeeeee......eeeeeeeeeee.......eeeeeeeeeeeee....eeeeeeehhhhh.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4mxv B   28 KPAAHLIGDPSKQNSLLWRANTDRAFLQDGFSLSNNSLLVPTSGIYFVYSQVVFSGKSSPLYLAHEVQLFSSQYPFHVPLLSSQKMVYPGLQEPWLHSMYHGAAFQLTQGDQLSTHTDGIPHLVLSPSTVFFGAFAL  171
                                    37        47        57        67        77      ||94       104       114       124       134       144       154       164       
                                                                                   84|                                                                               
                                                                                    92                                                                               


Chain D from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.........ee......eee...eee..eee....eeeeeeeeeeeee.......eeeeeee..eeeeeeee.........eeeeeeeeeeeee....eeeeeeehhhhh.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4mxv D   28 KPAAHLIGDPSKQNSLLWRANTDRAFLQDGFSLSNNSLLVPTSGIYFVYSQVVFSGKASSPLYLAHEVQLFHVPLLSSQKMVYPGLQEPWLHSMYHGAAFQLTQGDQLSTHTDGIPHLVLSPSTVFFGAFAL  171
                                    37        47        57        67        77       |93       103||     119       129       139       149       159       169  
                                                                                    85|         104|                                                            
                                                                                     92          111                                                            


Chain E from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee........eeeeeee...........eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4mxv E    1 DIQMTQSPSSLSASVGDRVTITCRASQAVSSAVAWYQQKPGKAPKLLIYSASHRYTGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQESYSTPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  211
                                    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:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee......eeeeeee....eeee.......eeeee.....eeeeee...hhhhheeeeeee........ee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4mxv F    1 EVQLVESGGGLVQPGGSLRLSCAASGYTFTSYVIHWVRQAPGKGLEWVGYNNPYNAGTNYNEKFKGRFTISSDKSKNTAYLQMNSLRAEDTAVYYCSRPTMLPWFAYWGQGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |  105       115       125 ||    141       151       161       171       181       191       201       211   
                                                                              52A                            82A||               100K                        127|                                                                                
                                                                                                              82B|                                            134                                                                                
                                                                                                               82C                                                                                                                               


Chain H from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee....eeeeeeeee..hhhhh.eeeeee......eeeeee......eee........eeeee....eeeeeee..hhhhheeeeeee........ee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4mxv H    1 EVQLVESGGGLVQPGGSLRLSCAASGYTFTSYVIHWVRQAPGKGLEWVGYNNPYNAGTNYNEKFKGRFTISSDKSKNTAYLQMNSLRAEDTAVYYCSRPTMLPWFAYWGQGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |  105       115       125 ||    141       151       161       171       181       191       201       211   
                                                                              52A                            82A||               100K                        127|                                                                                
                                                                                                              82B|                                            134                                                                                
                                                                                                               82C                                                                                                                               


Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee........eeeeeee...........eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....ee............eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4mxv L    1 DIQMTQSPSSLSASVGDRVTITCRASQAVSSAVAWYQQKPGKAPKLLIYSASHRYTGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQESYSTPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 


Chain X from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee.........eeeeee...........eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4mxv X    1 DIQMTQSPSSLSASVGDRVTITCRASQAVSSAVAWYQQKPGKAPKLLIYSASHRYTGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQESYSTPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 


Chain Y from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeee........ee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4mxv Y    1 EVQLVESGGGLVQPGGSLRLSCAASGYTFTSYVIHWVRQAPGKGLEWVGYNNPYNAGTNYNEKFKGRFTISSDKSKNTAYLQMNSLRAEDTAVYYCSRPTMLPWFAYWGQGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |  105       115       125 ||    141       151       161       171       181       191       201       211   
                                                                              52A                            82A||               100K                        127|                                                                                
                                                                                                              82B|                                            134                                                                                
                                                                                                               82C
   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 4MXV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MXV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MXV)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)

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  Ligands, Modified Residues, Ions
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  Sites
(no "Sites" information available for 4mxv)
 
  Cis Peptide Bonds
    Glu F:148 - Pro F:149   [ RasMol ]  
    Glu H:148 - Pro H:149   [ RasMol ]  
    Glu Y:148 - Pro Y:149   [ RasMol ]  
    Phe F:146 - Pro F:147   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Phe Y:146 - Pro Y:147   [ RasMol ]  
    Ser E:7 - Pro E:8   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Ser X:7 - Pro X:8   [ RasMol ]  
    Thr E:94 - Pro E:95   [ RasMol ]  
    Thr L:94 - Pro L:95   [ RasMol ]  
    Thr X:94 - Pro X:95   [ RasMol ]  
    Tyr A:108 - Pro A:109   [ RasMol ]  
    Tyr E:140 - Pro E:141   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
    Tyr X:140 - Pro X:141   [ RasMol ]  
 

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  4mxv
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 Related Entries

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

UniProtKB/Swiss-Prot
        TNFB_HUMAN | P01374: 1tnr 4mxw

(-) Related Entries Specified in the PDB File

1tnr 4mxw