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(-) Description

Title :  STRUCTURE OF PERTUZUMAB FAB WITH LIGHT CHAIN CLAMBDA AT 2.16A
 
Authors :  A. Pustilnik, S. M. Lewis, X. Wu, A. Sereno, F. Huang, G. Guntas, A. Leave E. M. Smith, C. Ho, C. Hansen-Estruch, A. K. Chamberlain, S. M. Truhlar B. Kuhlman, S. J. Demarest, S. Atwell
Date :  09 Jul 13  (Deposition) - 29 Jan 14  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.16
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Fab, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Lewis, X. Wu, A. Pustilnik, A. Sereno, F. Huang, H. L. Rick, G. Guntas, A. Leaver-Fay, E. M. Smith, C. Ho, C. Hansen-Estruch, A. K. Chamberlain, S. M. Truhlar, E. M. Conner, S. Atwell, B. Kuhlman, S. J. Demarest
Generation Of Bispecific Igg Antibodies By Structure-Based Design Of An Orthogonal Fab Interface.
Nat. Biotechnol. V. 32 191 2014
PubMed-ID: 24463572  |  Reference-DOI: 10.1038/NBT.2797

(-) Compounds

Molecule 1 - PERTUZUMAB FAB HEAVY CHAIN
    Chains: A, C
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Taxid: 9606
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - LIGHT CHAIN CLAMBDA
    Chains: B, D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Taxid: 9606
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:7 , GLY A:8 , LYS A:201BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWARELYS A:209 , ALA B:112 , ALA B:113 , HIS B:198 , HOH B:411 , HOH B:442BINDING SITE FOR RESIDUE ACT B 301
3AC3SOFTWAREGLU A:1 , ARG C:94 , TYR C:102 , HOH D:444BINDING SITE FOR RESIDUE SO4 C 301
4AC4SOFTWARESER A:25 , GLY A:26 , ASN A:76 , GLY D:57BINDING SITE FOR RESIDUE SO4 D 301

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:140 -A:196
3B:23 -B:88
4B:135 -B:194
5C:22 -C:92
6C:140 -C:196
7D:23 -D:88
8D:135 -D:194

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Phe A:146 -Pro A:147
2Glu A:148 -Pro A:149
3Ser B:7 -Pro B:8
4Tyr B:94 -Pro B:95
5Tyr B:141 -Pro B:142
6Phe C:146 -Pro C:147
7Glu C:148 -Pro C:149
8Ser D:7 -Pro D:8
9Tyr D:94 -Pro D:95
10Tyr D:141 -Pro D:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LLU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LLU)

(-) Exons   (0, 0)

(no "Exon" information available for 4LLU)

(-) 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:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeee..eeeeeee...eeeee........eeeeeeee........eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee..........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4llu A   1 EVQLVESGGGLVQPGGSLRLSCAASGFTFTDYTMDWVRQAPGKGLEWVADVNPNSGGSIYNQRFKGRFTLSVDRSKNTLYLQMNSLRAEDTAVYYCARNLGPSFYFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 214
                                    10        20        30        40        50  |     59        69        79   |||  86        96   ||  104       114       124       134       144       154       164       174       184       194       204       214
                                                                              52A                            82A||               99A|                                                                                                                   
                                                                                                              82B|                99B                                                                                                                   
                                                                                                               82C                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains d4llub1 B:1-107 automated matches                                                                          d4llub2 B:108-210 automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhh...eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4llu B   1 DIQMTQSPSSLSASVGDRVTITCKASQDVSIGVAWYQQKPGKAPKLLIYSASYRYTGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYYIYPYTFGQGTKVEIKGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT 210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210


Chain C from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee........eeeee....eeeeee...hhhhheeeeeeeee..eeeeeee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee........eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4llu C   1 EVQLVESGGGLVQPGGSLRLSCAASGFTFTDYTMDWVRQAPGKGLEWVADVNPNSGGSIYNQRFKGRFTLSVDRSKNTLYLQMNSLRAEDTAVYYCARNLGPSFYFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 214
                                    10        20        30        40        50  |     59        69        79   |||  86        96   ||  104       114       124       134       144       154       164       174       184       194       204       214
                                                                              52A                            82A||               99A|                                                                                                                   
                                                                                                              82B|                99B                                                                                                                   
                                                                                                               82C                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains d4llud1 D:1-106 automated matches                                                                         d4llud2 D:110-209 automated matches                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..ee.......eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee.........eeeeee...........eee.......eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4llu D   1 DIQMTQSPSSLSASVGDRVTITCKASQDVSIGVAWYQQKPGKAPKLLIYSASYRYTGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYYIYPYTFGQGTKVEIPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP 209
                                    10        20        30        40        50        60        70        80        90       100     ||113       123       133       143       153       163       173       183       193       203      
                                                                                                                                   106|                                                                                                   
                                                                                                                                    110
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  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  (1, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LLU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LLU)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        IGLC2_HUMAN | P0DOY2: 1jvk 1lil 1zvo 2jb5 2jb6 3c2a 3tv3 3twc 3tyg 4eow 4lld 4llm 4llq 4llw 4lly 4o58 4o5i 5d9q 5iq7 5iq9
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        S6C4R2_HUMAN | S6C4R2: 4ogx 4ogy 4pub

(-) Related Entries Specified in the PDB File

1s78 ERBB2-PERTUZUMAB COMPLEX
4lld WILD-TYPE CH1-CLAMBDA
4llm
4llq
4llw
4lly