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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  PD-L1 IN COMPLEX WITH BMS-936559 FAB
 
Authors :  Y. S. Heo
Date :  16 Jun 16  (Deposition) - 09 Nov 16  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Y. Lee, H. T. Lee, W. Shin, J. Chae, J. Choi, S. H. Kim, H. Lim, T. Won Heo, K. Y. Park, Y. J. Lee, S. E. Ryu, J. Y. Son, J. U. Lee, Y. S. Heo
Structural Basis Of Checkpoint Blockade By Monoclonal Antibodies In Cancer Immunotherapy
Nat Commun V. 7 13354 2016
PubMed-ID: 27796306  |  Reference-DOI: 10.1038/NCOMMS13354

(-) Compounds

Molecule 1 - PROGRAMMED CELL DEATH 1 LIGAND 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR PPPARG4
    Expression System Taxid1182032
    FragmentUNP RESIDUES 18-134
    GeneCD274, B7H1, PDCD1L1, PDCD1LG1, PDL1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROGRAMMED DEATH LIGAND 1,B7 HOMOLOG 1,B7-H1
 
Molecule 2 - IGG H CHAIN
    ChainsH
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES
 
Molecule 3 - IGK@ PROTEIN
    ChainsL
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit AHL

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5GGT)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GGT)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe H:156 -Pro H:157
2Glu H:158 -Pro H:159
3Ser L:7 -Pro L:8
4Tyr L:139 -Pro L:140

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GGT)

(-) 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:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee....eee..........hhhh.eeeeee.....eeee..ee.....hhhhh..eeee..hhhhh..eeee...hhhhheeeeeeee...eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 5ggt A  18 AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAP 133
                                    27        37        47        57        67        77        87        97       107       117       127      

Chain H from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee...eee.....eeeeeee.........eeeeee.....eeeeeee.......ee.......eeeeee....eeeeee...hhhhheeeeeee.............ee...eeeee........eeeee....eeeeeeeeeee.....eee.........eee...ee.....eeeeeeeeee.hhhhhh..eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ggt H   2 VQLVQSGAEVKKPGSSVKVSCKTSGDTFSTYAISWVRQAPGQGLEWMGGIIPIFGKAHYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYFCARKFHFVSGSPFGMDVWGQGTTVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 223
                                    11        21        31        41        51        61        71        81        91       101       111       121       131     ||147       157       167       177       187       197       207       217      
                                                                                                                                                                 137|                                                                               
                                                                                                                                                                  144                                                                               

Chain L from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.......eeee...ee.......eeee....eeeeee...hhhhh.eeeeee.....ee...eeeee.........eee..hhhhhh..eeeeeeeeeee.....eeeeee........ee............eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ggt L   1 EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 210
                                    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 5GGT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)

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Asymmetric/Biological Unit
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  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 5ggt)
 
  Sites
(no "Sites" information available for 5ggt)
 
  Cis Peptide Bonds
    Glu H:158 - Pro H:159   [ RasMol ]  
    Phe H:156 - Pro H:157   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Tyr L:139 - Pro L:140   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        PD1L1_HUMAN | Q9NZQ73bik 3bis 3fn3 3sbw 4z18 4zqk 5c3t 5grj 5ius 5j89 5j8o 5jdr 5jds 5n2d 5n2f

(-) Related Entries Specified in the PDB File

5ggq 5ggr 5ggs 5ggu 5ggv