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(-) Description

Title :  STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE CD40 IN COMPLEX WITH CHI220 FAB
 
Authors :  S. Sheriff
Date :  08 Sep 15  (Deposition) - 01 Jun 16  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.69
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Cell Surface Receptor, Antibody-Antigen Complex, Antitumor, Immune System-Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Yamniuk, A. Suri, S. R. Krystek, J. Tamura, V. Ramamurthy, R. Kuhn K. Carroll, C. Fleener, R. Ryseck, L. Cheng, Y. An, P. Drew, S. Grant, S. J. Suchard, S. G. Nadler, J. W. Bryson, S. Sheriff
Functional Antagonism Of Human Cd40 Achieved By Targeting A Unique Species-Specific Epitope.
J. Mol. Biol. V. 428 2860 2016
PubMed-ID: 27216500  |  Reference-DOI: 10.1016/J.JMB.2016.05.014

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 5
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: EXTRACELLULAR DOMAIN RESIDUES 23-193
    Gene: CD40, TNFRSF5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: B-CELL SURFACE ANTIGEN CD40,BP50,CD40L RECEPTOR,CDW40
 
Molecule 2 - CHI220 FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606
 
Molecule 3 - CHI220 FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP H:62 , ARG H:66binding site for residue SO4 H 301
2AC2SOFTWAREHIS L:53 , SER L:54binding site for residue SO4 L 301

(-) SS Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1A:26 -A:37
2A:38 -A:51
3A:41 -A:59
4A:62 -A:77
5A:83 -A:103
6A:105 -A:119
7A:111 -A:116
8H:22 -H:92
9H:142 -H:208
10L:23 -L:88
11L:134 -L:194

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Ala A:115 -Cys A:116
2Ser H:95 -Gly H:96
3Phe H:148 -Pro H:149
4Glu H:150 -Pro H:151
5Ser L:7 -Pro L:8
6Phe L:94 -Pro L:95
7Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DMI)

(-) 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:98
                                                                                                                                   
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................ee.............ee....ee..........ee....hhhhh.....................ee.......ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                5dmi A   24 TACREKQYLINSQCCSLCQPGQKLVSDCTEFTETECLPCGESEFLDTWNRETHCHQHKYCDPNLGLRVQQKGTSETDTICTCEEGWHCTSEACESCVL  121
                                    33        43        53        63        73        83        93       103       113        


Chain H from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeee............ee...eeeee........eeeee..........eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhhhhh...eeeeehhhheeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dmi H    1 QIQLVQSGPELKKPGETVRISCKASGYAFTTTGMQWVQEMPGKGLKWIGWINTHSGVPKYVEDFKGRFAFSLETSANTAYLQISNLKNEDTATYFCVRSGNGNYDLAYFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  228
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||101       111       121       131 ||    143       153||||   168||     179 ||    190     ||203       213       225   
                                                                              52A                            82A||               100A||||                              133|               154|||    169|       181|          196|||                 222|   
                                                                                                              82B|                100B|||                               136                156||     171        183           199||                  225   
                                                                                                               82C                 100C||                                                   157|                               200|                        
                                                                                                                                    100D|                                                    162                                202                        
                                                                                                                                     100E                                                                                                                  


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee........eeeeeee............eeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dmi L    1 DIVLTQSPATLSVTPGDRVSLSCRASQSISDYLHWYQQKSHESPRLLIKYASHSISGIPSRFSGSGSGSDFTLSINSVEPEDVGIYYCQHGHSFPWTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  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)
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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 5DMI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (51, 51)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:115 - Cys A:116   [ RasMol ]  
    Glu H:150 - Pro H:151   [ RasMol ]  
    Phe H:148 - Pro H:149   [ RasMol ]  
    Phe L:94 - Pro L:95   [ RasMol ]  
    Ser H:95 - Gly H:96   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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  TNR5_HUMAN | P25942
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 Related Entries

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

UniProtKB/Swiss-Prot
        TNR5_HUMAN | P25942: 1cdf 1czz 1d00 1fll 1lb6 3qd6 5dmj 5ihl

(-) Related Entries Specified in the PDB File

5dmj