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(-) Description

Title :  STRUCTURE OF PD-L1
 
Authors :  A. Zhou, H. Wei
Date :  17 Apr 16  (Deposition) - 12 Apr 17  (Release) - 12 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Immunosuppression, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Zhang, H. Wei, X. Wang, Y. Bai, P. Wang, J. Wu, X. Jiang, Y. Wang, H. Cai T. Xu, A. Zhou
Structural Basis Of A Novel Pd-L1 Nanobody For Immune Checkpoint Blockade.
Cell Discov V. 3 17004 2017
PubMed-ID: 28280600  |  Reference-DOI: 10.1038/CELLDISC.2017.4

(-) Compounds

Molecule 1 - PROGRAMMED CELL DEATH 1 LIGAND 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 18-239
    Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROGRAMMED DEATH LIGAND 1,B7 HOMOLOG 1,B7-H1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5JDR)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:40 -A:114
2A:155 -A:209
3B:40 -B:114
4B:155 -B:209

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:160 -Pro A:161
2Asp A:215 -Pro A:216
3Tyr B:160 -Pro B:161
4Asp B:215 -Pro B:216

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JDR)

(-) 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:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...eeeeeee............eeeeee..eeeeeee.........hhhhh..eee.hhhh...eeeeeee..hhhhheeeeeeee...eeeeeeeeeee......eeeeeeee....eeeeeeeeee....eeeeee....ee..eeeeee.......eeeeeeeeee.....eeeeeeee....eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jdr A  22 TVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYNKINQRILVVDPVTSEHELTCQAEGYPKAEVIWTSSDHQVLSGKTTTTNSKREEKLFNVTSTLRINTTTNEIFYCTFRRLDPEENHTAELVIPELP 230
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221         


Chain B from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee....eee...............eeeeee..eeeeeee..ee.....hhhhh..eeee..hhhhh..eeee........eeeeeeee...eeeeeeeeeee.....eeeeeeeee....eeeeeeeeee....eeeeee........eeeeee.......eeeeeeeeee.....eeeeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jdr B  19 FTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYNKINQRILVVDPVTSEHELTCQAEGYPKAEVIWTSSDHQVLSGKTTTTNSKREEKLFNVTSTLRINTTTNEIFYCTFRRLDPEENHTAELVIP 227
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218
   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 5JDR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:215 - Pro A:216   [ RasMol ]  
    Asp B:215 - Pro B:216   [ RasMol ]  
    Tyr A:160 - Pro A:161   [ RasMol ]  
    Tyr B:160 - Pro B: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 5grj 5ius 5j89 5j8o 5jds 5n2d 5n2f

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5JDR)