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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PD-L1 WITH MONOCLONAL ANTIBODY AVELUMAB
 
Authors :  K. Liu, S. Tan, Y. Chai, D. Chen, H. Song, C. W. -H. Zhang, Y. Shi, J. Liu, W. J. Lyu, S. Gao, J. Yan, J. Qi, G. F. Gao
Date :  11 Aug 16  (Deposition) - 02 Nov 16  (Release) - 18 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.21
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Pd-L1, Avelumab, Monoclonal Antibody, Tumor Immunothepapy, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Liu, S. Tan, Y. Chai, D. Chen, H. Song, C. W. Zhang, Y. Shi, J. Liu, W. Tan, J. Lyu, S. Gao, J. Yan, J. Qi, G. F. Gao
Structural Basis Of Anti-Pd-L1 Monoclonal Antibody Avelumab For Tumor Therapy.
Cell Res. V. 27 151 2017
PubMed-ID: 27573173  |  Reference-DOI: 10.1038/CR.2016.102

(-) Compounds

Molecule 1 - AVELUMAB H CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - AVELUMAB L CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - PROGRAMMED CELL DEATH 1 LIGAND 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 18-238
    Gene: PDL1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HUMAN PD-L1

 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 5GRJ)

(-) Sites  (0, 0)

(no "Site" information available for 5GRJ)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:40 -A:114
2A:155 -A:209
3H:22 -H:96
4L:22 -L:90

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:160 -Pro A:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GRJ)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee....eeeeee............eeeeee..eeeeeee..ee.....hhhhh..eee..hhhhh.eeeeee........eeeeeeee...eeeeeeeeeee......eeeeeeee....eeeeeeeeee...eeeeeee....ee..eeeeee....eeeeeeeeee.....eeeeeeee....eeeeeeee.....ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5grj A  18 AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYNKINQRILVVDPVTSEHELTCQAEGYPKAEVIWTSSDHQVLSGKTTTTNSEKLFNVTSTLRINTTTNEIFYCTFRRLDPEENHTAELVIPELPLAH 233
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177      |190       200       210       220       230   
                                                                                                                                                                                                184|                                             
                                                                                                                                                                                                 188                                             


Chain H from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.........eeeeeeeee..hhhhheeeeeee.....eeeeeee......eee.......eeeeee....eeeeeee........eeeeeee.......eeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 5grj H   1 EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYIMMWVRQAPGKGLEWVSSIYPSGGITFYADTVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARIKLGTVTTVDYWGQGTLVTV 118
                                    10        20        30        40        50        60        70        80        90       100       110        


Chain L from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eee......eeeeee...........eeeeee......eeee.............eeeeee..eeeeee.........eeeeeee.....eee...eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 5grj L   2 SALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYDVSNRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTSSSTRVFGTGTKVTV 109
                                    11        21        31        41        51        61        71        81        91       101
   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 5GRJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Tyr A:160 - Pro A:161   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        PD1L1_HUMAN | Q9NZQ7: 3bik 3bis 3fn3 3sbw 4z18 4zqk 5c3t 5ggt 5ius 5j89 5j8o 5jdr 5jds 5n2d 5n2f

(-) Related Entries Specified in the PDB File

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