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(-) Description

Title :  CRYSTAL STRUCTURE OF PERTUZUMAB CLAMBDA FAB WITH VARIABLE DOMAIN REDESIGN (VRD2) AT 1.95A
 
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 :  1.95
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 - MUTATED 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  (1, 11)

Asymmetric Unit (1, 11)
No.NameCountTypeFull Name
1SO411Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 2 (1, 7)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:39 , PRO A:41 , GLY A:42 , LYS A:43 , GLY A:44 , TYR B:87 , LYS B:103 , HOH B:422 , HOH B:467BINDING SITE FOR RESIDUE SO4 A 501
02AC2SOFTWAREVAL A:72 , ASP A:73 , ARG A:74 , SER A:75BINDING SITE FOR RESIDUE SO4 A 502
03AC3SOFTWAREPHE A:27 , THR A:28 , TYR A:32BINDING SITE FOR RESIDUE SO4 A 503
04AC4SOFTWAREHIS A:170 , SER B:138BINDING SITE FOR RESIDUE SO4 B 301
05AC5SOFTWAREHIS C:170 , HOH C:629 , GLN D:168 , SER D:169BINDING SITE FOR RESIDUE SO4 C 501
06AC6SOFTWAREGLN C:177 , SER C:178 , HOH C:616 , GLY D:159 , GLU D:161BINDING SITE FOR RESIDUE SO4 C 502
07AC7SOFTWARELYS C:149 , ASP C:150 , GLN C:177 , LYS D:130BINDING SITE FOR RESIDUE SO4 C 503
08AC8SOFTWAREASP C:73 , ARG C:74 , SER C:75BINDING SITE FOR RESIDUE SO4 C 504
09AC9SOFTWAREPHE C:27 , THR C:28 , TYR C:32BINDING SITE FOR RESIDUE SO4 C 505
10BC1SOFTWAREPRO D:59 , ARG D:61 , GLU D:81BINDING SITE FOR RESIDUE SO4 D 301
11BC2SOFTWARETYR C:39 , ARG D:38 , PRO D:40 , GLY D:41 , HOH D:476BINDING SITE FOR RESIDUE SO4 D 302

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:96
2A:146 -A:202
3B:23 -B:88
4B:135 -B:194
5C:22 -C:96
6C:146 -C:202
7D:23 -D:88
8D:135 -D:194

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Phe A:152 -Pro A:153
2Glu A:154 -Pro A:155
3Ser B:7 -Pro B:8
4Tyr B:94 -Pro B:95
5Lys C:43 -Gly C:44
6Phe C:152 -Pro C:153
7Glu C:154 -Pro C:155
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 4LLW)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LLW)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeeee....eeee.......eeeeeehhh.eeeeee...hhhhheeeeeeee......eeee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4llw A   1 EVQLVESGGGLVQPGGSLRLSCAASGFTFTDYTMDWVRYAPGKGLEWVADVNPNSGGSIYNQRFKGRFTLSVDRSKNTLYLQMNSLRAEDTAVYYCARNLGPSFYFDYWGQGTLVTVSSASTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 ||    147       157       167       177       187       197       207       217   
                                                                                                                                                             132|                                                                                
                                                                                                                                                              140                                                                                


Chain B from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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...eeeeeeee.....eeeeeee..eeeeeeee..ee....eeeeeeee.hhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4llw B   1 DIQMTQSPSSLSASVGDRVTITCKASQDVSIGVAWYQRKPGKAPKLLIYSASYRYTGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYYIYPYTFGQGTKVEIKGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT 210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      |173       183       193       203       
                                                                                                                                                                                                167|                                       
                                                                                                                                                                                                 171                                       


Chain C from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeee..eeeeeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhhh..eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4llw C   1 EVQLVESGGGLVQPGGSLRLSCAASGFTFTDYTMDWVRYAPGKGLEWVADVNPNSGGSIYNQRFKGRFTLSVDRSKNTLYLQMNSLRAEDTAVYYCARNLGPSFYFDYWGQGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  ||   146       156       166       176       186       196       206       216    
                                                                                                                                                              133|                                                                                
                                                                                                                                                               140                                                                                


Chain D from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4llw D   1 DIQMTQSPSSLSASVGDRVTITCKASQDVSIGVAWYQRKPGKAPKLLIYSASYRYTGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYYIYPYTFGQGTKVEIKGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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 4LLW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

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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 4llu 4lly 4o58 4o5i 5d9q 5iq7 5iq9
        S6B291_HUMAN | S6B291: 3mnw 3mnz 4eow 5c7k 5cus 5d9q 5veb 5vic 5vig 5viy 5vj6 5vob 5voc 5vod
UniProtKB/TrEMBL
        S6B291_HUMAN | S6B291: 4lly 4oqt 4ydv

(-) Related Entries Specified in the PDB File

4lld CH1-CL
4llm
4llq
4llu PARENT PERTUZUMAB CLAMBDA
4lly