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(-) Description

Title :  STRUCTURE OF HUMAN PROGRAMMED CELL DEATH 1 LIGAND 1 (PD-L1) WITH LOW MOLECULAR MASS INHIBITOR
 
Authors :  K. M. Zak, P. Grudnik, K. Guzik, B. J. Zieba, B. Musielak, P. Doemling, G. T. A. Holak
Date :  07 Apr 16  (Deposition) - 27 Apr 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Pd-L1, Programmed Cell Death 1 Ligand 1, Cell Cycle, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Zak, P. Grudnik, K. Guzik, B. J. Zieba, B. Musielak, A. Domling, G. Dubin, T. A. Holak
Structural Basis For Small Molecule Targeting Of The Programmed Death Ligand 1 (Pd-L1).
Oncotarget V. 7 30323 2016
PubMed-ID: 27083005  |  Reference-DOI: 10.18632/ONCOTARGET.8730

(-) Compounds

Molecule 1 - PROGRAMMED CELL DEATH 1 LIGAND 1
    Chains: C, A, D, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):   CD
Biological Unit 2 (1x): AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
16GX2Ligand/IonN-{2-[({2-METHOXY-6-[(2-METHYL[1,1'-BIPHENYL]-3-YL)METHOXY]PYRIDIN-3-YL}METHYL)AMINO]ETHYL}ACETAMIDE
2EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
16GX1Ligand/IonN-{2-[({2-METHOXY-6-[(2-METHYL[1,1'-BIPHENYL]-3-YL)METHOXY]PYRIDIN-3-YL}METHYL)AMINO]ETHYL}ACETAMIDE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
16GX1Ligand/IonN-{2-[({2-METHOXY-6-[(2-METHYL[1,1'-BIPHENYL]-3-YL)METHOXY]PYRIDIN-3-YL}METHYL)AMINO]ETHYL}ACETAMIDE
2EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR C:20 , TYR C:56 , MET C:115 , ALA C:121 , ASP C:122 , TYR C:123 , LYS C:124 , HOH C:307 , ILE D:54 , TYR D:56 , GLN D:66 , MET D:115 , ILE D:116 , SER D:117binding site for residue 6GX C 201
2AC2SOFTWAREPRO A:133 , ALA A:135 , ALA A:136 , HOH A:303 , HOH A:353binding site for residue EDO A 201
3AC3SOFTWARETHR A:20 , TYR A:56 , MET A:115 , ALA A:121 , ASP A:122 , TYR A:123 , HOH A:301 , TYR B:56 , GLN B:66 , MET B:115 , ILE B:116 , SER B:117binding site for residue 6GX B 201

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:40 -A:114
2B:40 -B:114
3C:40 -C:114
4D:40 -D:114

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu D:138 -Glu D:139

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J89)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J89)

(-) Exons   (0, 0)

(no "Exon" information available for 5J89)

(-) Sequences/Alignments

Asymmetric 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:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee....eee..........hhhh.eeeeee..eeeeeee.........hhhhh..eeeehhhhhhh..eeee...hhhhheeeeeeee...eeeeeeeeeee.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j89 A  18 AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYAAALEHHHHH 144
                                    27        37        47        57        67        77        87        97       107       117       127       137       


Chain B from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee....eee..........hhhh.eeeeee..eeeeeee..ee.....hhhhh..eee.hhhhhhh...eee...hhhhheeeeeeee...eeeeeeeeeee.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j89 B  18 AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYAAALEHHH 142
                                    27        37        47        57        67        77        87        97       107       117       127       137     


Chain C from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee....eeeeee.......hhhh.eeeeee..eeeeeee..ee.....hhhhh..eeehhhhhh..eeeeee...hhhhheeeeeeee...eeeeeeeeeee.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j89 C  18 AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYAAALEHHH 142
                                    27        37        47        57        67        77        87        97       107       117       127       137     


Chain D from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee....eee..........hhhh.eeeeee..eeeeeee..ee.hhhhhhhhh..eeehhhhhh.....eee...hhhhheeeeeeee...eeeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j89 D  18 AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYAAALEHH 141
                                    27        37        47        57        67        77        87        97       107       117       127       137
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 5J89)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J89)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J89)

(-) Gene Ontology  (24, 24)

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 Related Entries

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

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