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(-) Description

Title :  CRYSTAL STRUCTURE OF PEMBROLIZUMAB, A FULL LENGTH IGG4 ANTIBODY
 
Authors :  G. Scapin, W. Prosise, P. Reichert
Date :  02 Sep 15  (Deposition) - 18 Nov 15  (Release) - 03 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym./Biol. Unit :  A,B,F,G
Keywords :  Cancer, Antibody, Subclasses, Igg4, Melanoma, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Scapin, X. Yang, W. W. Prosise, M. Mccoy, P. Reichert, J. M. Johnston R. S. Kashi, C. Strickland
Structure Of Full-Length Human Anti-Pd1 Therapeutic Igg4 Antibody Pembrolizumab.
Nat. Struct. Mol. Biol. V. 22 953 2015
PubMed-ID: 26595420  |  Reference-DOI: 10.1038/NSMB.3129

(-) Compounds

Molecule 1 - LIGHT CHAIN
    Chains: A, F
    Engineered: YES
    Expression System: MAMMALIA
    Expression System Taxid: 40674
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - HEAVY CHAIN
    Chains: B, G
    Engineered: YES
    Expression System: MAMMALIA
    Expression System Taxid: 40674
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 22)

Asymmetric/Biological Unit (6, 22)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2FUC1Ligand/IonALPHA-L-FUCOSE
3MAN4Ligand/IonALPHA-D-MANNOSE
4NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO45Ligand/IonSULFATE ION
6SUC3Ligand/IonSUCROSE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:49 , PRO A:63 , ARG A:65 , GLU A:85binding site for residue SO4 A 301
02AC2SOFTWARETYR B:27 , THR B:28 , ASN B:31 , TYR B:32binding site for residue SO4 B 501
03AC3SOFTWARELYS B:360 , ASN B:361 , GLN B:362 , SUC B:513binding site for residue SO4 B 502
04AC4SOFTWAREGLU A:169 , ASP A:171 , HOH A:436 , HIS B:171 , HOH B:618 , HOH B:623 , HOH B:711binding site for residue SO4 B 503
05AC5SOFTWARETRP B:313 , LYS B:338 , ALA B:339binding site for residue SO4 B 504
06AC6SOFTWAREARG B:38 , GLN B:43 , ASP B:89 , ILE B:377 , ALA B:378 , VAL B:379 , LYS B:392 , THR B:393 , PRO B:395 , PRO B:396 , HOH B:602 , HOH B:603 , HOH B:613 , HOH B:637 , HOH B:650binding site for residue SUC B 512
07AC7SOFTWARELYS B:360 , GLN B:362 , ASN B:390 , ARG B:409 , THR B:411 , SO4 B:502 , HOH B:617 , HOH B:660 , ARG G:344 , GLN G:347 , LYS G:370 , ASP G:399 , SER G:400 , ASP G:401binding site for residue SUC B 513
08AC8SOFTWAREPHE G:88 , LEU G:177 , SER G:179 , HOH G:614 , HOH G:632binding site for residue SUC G 508
09AC9SOFTWAREGLN B:274 , ASN B:276 , TYR B:278 , SER B:324 , PHE G:241 , PHE G:243 , THR G:260 , VAL G:264 , ASP G:265 , GLN G:295 , ASN G:297 , THR G:299 , ARG G:301binding site for Poly-Saccharide residues NAG G 501 through FUC G 507 bound to ASN G 297
10AD1SOFTWARESER B:141 , PHE B:241 , PHE B:243 , PRO B:247 , VAL B:264 , ASP B:265 , ASN B:297 , THR B:299 , ARG B:301binding site for Poly-Saccharide residues NAG B 505 through NAG B 511

(-) SS Bonds  (16, 16)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:92
2A:138 -A:198
3A:218 -B:134
4B:22 -B:96
5B:147 -B:203
6B:226 -G:226
7B:229 -G:229
8B:261 -B:321
9B:367 -B:425
10F:23 -F:92
11F:138 -F:198
12F:218 -G:134
13G:22 -G:96
14G:147 -G:203
15G:261 -G:321
16G:367 -G:425

(-) Cis Peptide Bonds  (21, 21)

Asymmetric/Biological Unit
No.Residues
1Ser A:7 -Pro A:8
2Leu A:98 -Pro A:99
3Tyr A:144 -Pro A:145
4Thr B:138 -Ser B:139
5Phe B:153 -Pro B:154
6Glu B:155 -Pro B:156
7Tyr B:222 -Gly B:223
8Pro B:224 -Pro B:225
9Lys B:246 -Pro B:247
10Leu B:251 -Met B:252
11Ser B:254 -Arg B:255
12Gln B:295 -Phe B:296
13Tyr B:373 -Pro B:374
14Ser F:7 -Pro F:8
15Leu F:98 -Pro F:99
16Tyr F:144 -Pro F:145
17Ala G:121 -Ser G:122
18Phe G:153 -Pro G:154
19Glu G:155 -Pro G:156
20Pro G:224 -Pro G:225
21Tyr G:373 -Pro G:374

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DK3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DK3)

(-) Exons   (0, 0)

(no "Exon" information available for 5DK3)

(-) 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:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee....ee..ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dk3 A   1 EIVLTQSPATLSLSPGERATLSCRASKGVSTSGYSYLHWYQQKPGQAPRLLIYLASYLESGVPARFSGSGSGTDFTLTISSLEPEDFAVYYCQHSRDLPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        


Chain B from PDB  Type:PROTEIN  Length:441
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhh.eeeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeee......eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeeee................eeeee..............eeeeeeeee......eeeeeee..eee...ee..........eeeeeeee...hhhhhh..eeeeeee......eeeee..........eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee...eee...ee.....eeeeeeeeeehhhhhh...eeeeee...hhhhheeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dk3 B   1 QVQLVQSGVEVKKPGASVKVSCKASGYTFTNYYMYWVRQAPGQGLEWMGGINPSNGGTNFNEKFKNRVTLTTDSSTTTAYMELKSLQFDDTAVYYCARRDYRFDMGFDYWGQGTTVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESKYGPPCPPCEFLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSQEDPEVQFNWYVDGVEVHNAKTKPREEQFNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLS 444
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443 
                                                                                                                                                                                                                                                              229|                                                                                                                                                                                                                   
                                                                                                                                                                                                                                                               233                                                                                                                                                                                                                   


Chain F from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee....ee..ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dk3 F   1 EIVLTQSPATLSLSPGERATLSCRASKGVSTSGYSYLHWYQQKPGQAPRLLIYLASYLESGVPARFSGSGSGTDFTLTISSLEPEDFAVYYCQHSRDLPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        


Chain G from PDB  Type:PROTEIN  Length:438
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhh.eeeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeee.............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeeee.............eeeee..hhhhhhh.....eeeeeeeee.......eeeeee..eee...ee...ee.....eeeeeeee.hhhhhhh...eeeeee.......eeeee..........eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee...eee...ee.....eeeeeeeeeehhhhhh...eeeeee...hhhhheeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dk3 G   1 QVQLVQSGVEVKKPGASVKVSCKASGYTFTNYYMYWVRQAPGQGLEWMGGINPSNGGTNFNEKFKNRVTLTTDSSTTTAYMELKSLQFDDTAVYYCARRDYRFDMGFDYWGQGTTVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESKYGPPCPPCGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSQEDPEVQFNWYVDGVEVHNAKTKPREEQFNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLS 444
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436        
                                                                                                                                                                                                                                                              229|                                                                                                                                                                                                                
                                                                                                                                                                                                                                                               236
   Legend:   → Mismatch (orange background)
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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 5DK3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DK3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DK3)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5DK3)

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