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(-) Description

Title :  PD-1 IN COMPLEX WITH NIVOLUMAB FAB
 
Authors :  Y. S. Heo
Date :  16 Jun 16  (Deposition) - 09 Nov 16  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B,H,L,Y,Z
Biol. Unit 1:  A,B,Y  (1x)
Biol. Unit 2:  H,L,Z  (1x)
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 - HEAVY CHAIN
    Chains: A, H
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 2 - LIGHT CHAIN
    Chains: B, L
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 3 - PROGRAMMED CELL DEATH PROTEIN 1
    Chains: Y, Z
    Engineered: YES
    Expression System: ESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR PPPARG4
    Expression System Taxid: 1182032
    Fragment: UNP RESIDUES 26-150
    Gene: PDCD1, PD1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HPD-1

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABHLYZ
Biological Unit 1 (1x): AB  Y 
Biological Unit 2 (1x):   HL Z

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5GGR)

(-) SS Bonds  (7, 7)

Asymmetric Unit
No.Residues
1A:22 -A:96
2B:23 -B:88
3B:134 -B:194
4H:22 -H:96
5H:140 -H:196
6L:23 -L:88
7Z:54 -Z:123

(-) Cis Peptide Bonds  (14, 14)

Asymmetric Unit
No.Residues
1Phe A:146 -Pro A:147
2Glu A:148 -Pro A:149
3Ser B:7 -Pro B:8
4Trp B:94 -Pro B:95
5Tyr B:140 -Pro B:141
6Phe H:146 -Pro H:147
7Glu H:148 -Pro H:149
8Ser L:7 -Pro L:8
9Trp L:94 -Pro L:95
10Tyr L:140 -Pro L:141
11Ser Y:38 -Pro Y:39
12Phe Y:82 -Pro Y:83
13Ser Z:38 -Pro Z:39
14Phe Z:82 -Pro Z:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GGR)

(-) 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:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....eeeeeeee........eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee........eeeee........eeeee.......eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhh....eeeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ggr A   2 VQLVESGGGVVQPGRSLRLDCKASGITFSNSGMHWVRQAPGKGLEWVAVIWYDGSKRYYADSVKGRFTISRDNSKNTLFLQMNSLRAEDTAVYYCATNDDYWGQGTLVTVSSASTKGPSVFPLAPSSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 213
                                    11        21        31        41        51        61        71        81        91       101       111       121      |134       144       154       164       174       184       194       204         
                                                                                                                                                        128|                                                                                 
                                                                                                                                                         132                                                                                 


Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee............eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee....eeeeeee......................eeeeeeeeeehhhhhh..eeeeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ggr B   1 EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQSSNWPRTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  


Chain H from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee....eeeeeeeee.........eeeee.....eeeeeeee..eeeeee........eeeee....eeeeeee..hhhhheeee...........eeeee........eeeee.....eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhhh...eeeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ggr H   2 VQLVESGGGVVQPGRSLRLDCKASGITFSNSGMHWVRQAPGKGLEWVAVIWYDGSKRYYADSVKGRFTISRDNSKNTLFLQMNSLRAEDTAVYYCATNDDYWGQGTLVTVSSASTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 213
                                    11        21        31        41        51        61        71        81        91       101       111       121      |136       146       156       166       176       186       196       206       
                                                                                                                                                        128|                                                                               
                                                                                                                                                         134                                                                               


Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee........eeeee......eeeee............eeeeee..eeeeee...hhhhh.eeeee............eeeee.......eeeee....hhhhhh...eeeeeeee.....eeeeee........eeeee.........eeeeeee..hhhhhh....eeeeee.......eee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ggr L   1 EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQSSNWPRTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  


Chain Y from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeee....eeeeee.......eeeeeee.....eeeeee.............eeee.....eeeeee........eeeeeeeee......eee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 5ggr Y  27 SPDRPWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPQTDKLAAFPEDRSQPGQDSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTE 146
                                    36        46        56        66     || 78        88        98       108       118       128       138        
                                                                        72|                                                                       
                                                                         75                                                                       


Chain Z from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee..eeeee....eeeeee.......eeeeeee....eeeeee............eeeee.....eeeeee.........eeeeeeee......eee...eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 5ggr Z  27 SPDRPWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSQTDKLAAFPEDRSQPGQDSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTE 146
                                    36        46        56        66    ||  79        89        99       109       119       129       139       
                                                                       71|                                                                       
                                                                        75
   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 5GGR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu A:148 - Pro A:149   [ RasMol ]  
    Glu H:148 - Pro H:149   [ RasMol ]  
    Phe A:146 - Pro A:147   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Phe Y:82 - Pro Y:83   [ RasMol ]  
    Phe Z:82 - Pro Z:83   [ RasMol ]  
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    Ser Y:38 - Pro Y:39   [ RasMol ]  
    Ser Z:38 - Pro Z:39   [ RasMol ]  
    Trp B:94 - Pro B:95   [ RasMol ]  
    Trp L:94 - Pro L:95   [ RasMol ]  
    Tyr B:140 - Pro B:141   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 
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 Related Entries

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

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        PDCD1_HUMAN | Q15116: 2m2d 3rrq 4zqk 5b8c 5ggs 5ius 5jxe 5wt9

(-) Related Entries Specified in the PDB File

5ggq 5ggs 5ggt 5ggu 5ggv