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(-) Description

Title :  CRYSTAL STRUCTURE OF ONARTUZUMAB FAB IN COMPLEX WITH MET AND HGF-BETA
 
Authors :  X. Ma, M. A. Starovasnik
Date :  10 Apr 13  (Deposition) - 28 Aug 13  (Release) - 20 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,H,L
Keywords :  Antibody, Glycosylation, Transferase-Immune System-Growth Factor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Merchant, X. Ma, H. R. Maun, Z. Zheng, J. Peng, M. Romero, A. Huang, N. Y. Yang, M. Nishimura, J. Greve, L. Santell, Y. W. Zhang, Y. Su, D. W. Kaufman, K. L. Billeci, E. Mai, B. Moffat, A. Lim, E. T. Duenas, H. S. Phillips, H. Xiang, J. C. Young, G. F. Vande Woude, M. S. Dennis, D. E. Reilly, R. H. Schwall, M. A. Starovasnik, R. A. Lazarus, D. G. Yansura
Monovalent Antibody Design And Mechanism Of Action Of Onartuzumab, A Met Antagonist With Anti-Tumor Activity As A Therapeutic Agent.
Proc. Natl. Acad. Sci. Usa V. 110 E2987 2013
PubMed-ID: 23882082  |  Reference-DOI: 10.1073/PNAS.1302725110

(-) Compounds

Molecule 1 - HEPATOCYTE GROWTH FACTOR
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Fragment: UNP RESIDUES 495-721
    Gene: HGF, HPTA
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HEPATOPOIETIN-A, SCATTER FACTOR, SF, HEPATOCYTE GROWTH FACTOR ALPHA CHAIN, HEPATOCYTE GROWTH FACTOR BETA CHAIN
 
Molecule 2 - HEPATOCYTE GROWTH FACTOR BETA CHAIN
    Chains: B
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Fragment: SEMA AND PSI DOMAIN, UNP RESIDUES 39-564
    Gene: MET
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HGF RECEPTOR, HGF/SF RECEPTOR, PROTO-ONCOGENE C-MET, SCATTER FACTOR RECEPTOR, SF RECEPTOR, TYROSINE-PROTEIN KINASE MET
 
Molecule 3 - ONARTUZUMAB FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606
 
Molecule 4 - ONARTUZUMAB FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN B:42 , LEU B:43 , ASN B:45 , HOH B:957BINDING SITE FOR RESIDUE NAG B 801

(-) SS Bonds  (18, 18)

Asymmetric/Biological Unit
No.Residues
1A:519 -A:535
2A:612 -A:679
3A:642 -A:658
4A:669 -A:697
5B:95 -B:101
6B:98 -B:160
7B:133 -B:141
8B:172 -B:175
9B:298 -B:363
10B:385 -B:397
11B:520 -B:538
12B:526 -B:561
13B:529 -B:545
14B:541 -B:551
15H:22 -H:92
16H:140 -H:196
17L:23 -L:88
18L:134 -L:194

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Gly B:87 -Pro B:88
2Phe H:146 -Pro H:147
3Glu H:148 -Pro H:149
4Ser L:7 -Pro L:8
5Tyr L:94 -Pro L:95
6Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K3J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K3J)

(-) Exons   (0, 0)

(no "Exon" information available for 4K3J)

(-) 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:227
                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.......eeeeee..eeeeeeeeee..eeeee.hhh...hhh.eeeee..............eeeeeeeeee......eeeeee..........................eeeeee.............eeeeeeeehhhhhhhhh.........eeeee...............eeee......eeeeee............eeeee...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4k3j A  495 VVNGIPTRTNIGWMVSLRYRNKHICGGSLIKESWVLTARQCFPSRDLKDYEAWLGIHDVHGRGDEKCKQVLNVSQLVYGPEGSDLVLMKLARPAVLDDFVSTIDLPNYGSTIPEKTSCSVYGWGYTGLINYDGLLRVAHLYIMGNEKCSQHHRGKVTLNESEICAGAEKIGSGPCEGDYGGPLVCEQHKMRMVLGVIVPGRGCAIPNRPGIFVRVAYYAKWIHKIIL  721
                                   504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       


Chain B from PDB  Type:PROTEIN  Length:499
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee....eeeeeee..eeeeee..eeeeee.....eeeeee...eee...................eee...eeeeeee.....eeeeee.hhhh.eeeee............eee.....................eeeeeeee..eeeeeeee..............eeeeee......ee......ee..hhhhh.....eeeeeeee..eeeeeeeee.......eeeeeeeee......eeeeeeeeeeee..eee.eeeeeeee..hhhhhhhhh......eeeeeeeee......eeeeeeeeeeehhhhhhhhhh..hhh.eee...............eee...eeee...........eeeeeeeee..eeeeeeee...eeeeee..........eeee..........eee......eeeeee..eeeeee..hhhhhh..hhhhhhhhhhhh.eeee..eeee.hhh....ee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4k3j B   39 MKYQLPNFTAETPIQNVILHEHHIFLGATNYIYVLNEEDLQKVAEYKTGPVLEHPDCFPCQDCSSKANLSGGVWKDNINMALVVDTYYDDQLISCGSVNRGTCQRHVFPHNHTADIQSEVHCIFSPQIEEPSQCPDCVVSALGAKVLSSVKDRFINFFVGNTINSSYFPDHPLHSISVRRLKETKDGFMFLTDQSYIDVLPEFRDSYPIKYVHAFESNNFIYFLTVQRETLDAQTFHTRIIRFCSINSGLHSYMEMPLECILTKEVFNILQAAYVSKPGAQLARQIGASLNDDILFGVFAQSKPDSAEPMDRSAMCAFPIKYVNDFFNKIVNKNNVRCLQHFYGPNHEHCEYRTEFTTALQRVDLFMGQFSEVLLTSISTFIKGDLTIANLGTSEGRFMQVVVSRSGPSTPHVNFLLDSHPVSPEVIVEHTLNNGYTLVITGKKITKIPLNGLGCRHFQSCSQCLSAPPFVQCGWCHDKCVRSEECLSGTWTQQICLPA  564
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298  ||   317       327       337       347       357       367       377       387       397|      424       434       444       454       464       474       484       494  ||   505       515       525       535       545       555         
                                                                                                                                                                                                                                                                                                301|                                                                                   397|                                                                               497|                                                                 
                                                                                                                                                                                                                                                                                                 311                                                                                    415                                                                                499                                                                 


Chain H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeee.........ee...eeeee........eeeee..........eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhh....eeeeeee....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4k3j H    1 EVQLVESGGGLVQPGGSLRLSCAASGYTFTSYWLHWVRQAPGKGLEWVGMIDPSNSDTRFNPNFKDRFTISADTSKNTAYLQMNSLRAEDTAVYYCATYRSYVTPLDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  215
                                    10        20        30        40        50  |     59        69        79   |||  86        96    || 104       114       124       134       144       154       164       174       184       194       204       214 
                                                                              52A                            82A||               100A|                                                                                                                   
                                                                                                              82B|                100B                                                                                                                   
                                                                                                               82C                                                                                                                                       


Chain L from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4k3j L    1 DIQMTQSPSSLSASVGDRVTITCKSSQSLLYTSSQKNYLAWYQQKPGKAPKLLIYWASTRESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYYAYPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  211
                                    10        20       27C|||     34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       
                                                     27A|||||                                                                                                                                                                                        
                                                      27B||||                                                                                                                                                                                        
                                                       27C|||                                                                                                                                                                                        
                                                        27D||                                                                                                                                                                                        
                                                         27E|                                                                                                                                                                                        
                                                          27F
   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 4K3J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K3J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K3J)

(-) Gene Ontology  (71, 80)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        HGF_HUMAN | P14210: 1bht 1gmn 1gmo 1gp9 1nk1 1shy 1si5 2ced 2cee 2ceg 2hgf 2qj2 3hms 3hmt 3hn4 3mkp 3sp8 4d3c 4o3t 4o3u 5coe 5cp9 5cs1 5cs3 5cs5 5cs9 5csq 5ct1 5ct2 5ct3
        MET_HUMAN | P08581: 1fyr 1r0p 1r1w 1shy 1ssl 1ux3 2cew 2g15 2rfn 2rfs 2uzx 2uzy 2wd1 2wgj 2wkm 3a4p 3bux 3c1x 3ccn 3cd8 3ce3 3cth 3ctj 3dkc 3dkf 3dkg 3efj 3efk 3f66 3f82 3i5n 3l8v 3lq8 3q6u 3q6w 3qti 3r7o 3rhk 3u6h 3u6i 3vw8 3zbx 3zc5 3zcl 3zxz 3zze 4aoi 4ap7 4deg 4deh 4dei 4eev 4gg5 4gg7 4iwd 4knb 4mxc 4o3t 4o3u 4r1v 4r1y 4xmo 4xyf 5dg5 5eob 5eyc 5eyd 5hlw 5hni 5ho6 5hoa 5hor 5hti 5t3q 5uab 5uad 5uaf

(-) Related Entries Specified in the PDB File

1shy