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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF HER2 WITH AN FAB
 
Authors :  W. Y. Fu, Y. X. Wang, L. J. Zhou
Date :  20 Mar 14  (Deposition) - 25 Mar 15  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Kinase, Transferase-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Fu, Y. Wang, Y. Zhang, L. Xiong, H. Takeda, L. Ding, Q. Xu, L. He, W. Tan A. N. Bethune, L. Zhou
Insights Into Her2 Signaling From Step-By-Step Optimization Of Anti-Her2 Antibodies.
Mabs V. 6 978 2014
PubMed-ID: 24838231  |  Reference-DOI: 10.4161/MABS.28786

(-) Compounds

Molecule 1 - RECEPTOR TYROSINE-PROTEIN KINASE ERBB-2
    Chains: A
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Plasmid: PLASMID
    Expression System Taxid: 10029
    Fragment: UNP RESIDUES 23-586
    Gene: ERBB2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: METASTATIC LYMPH NODE GENE 19 PROTEIN, MLN 19, PROTO- ONCOGENE NEU, PROTO-ONCOGENE C-ERBB-2, TYROSINE KINASE-TYPE CELL SURFACE RECEPTOR HER2, P185ERBB2
 
Molecule 2 - ANTIBODY LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Plasmid: PLASMID
    Expression System Taxid: 10029
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - ANTIBODY HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Plasmid: PLASMID
    Expression System Taxid: 10029
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3WSQ)

(-) Sites  (0, 0)

(no "Site" information available for 3WSQ)

(-) SS Bonds  (25, 25)

Asymmetric/Biological Unit
No.Residues
1A:4 -A:31
2A:140 -A:170
3A:173 -A:182
4A:177 -A:190
5A:198 -A:205
6A:202 -A:213
7A:214 -A:222
8A:218 -A:230
9A:233 -A:242
10A:246 -A:273
11A:277 -A:289
12A:293 -A:309
13A:312 -A:316
14A:320 -A:345
15A:453 -A:482
16A:489 -A:498
17A:493 -A:506
18A:509 -A:518
19A:522 -A:538
20A:541 -A:554
21A:545 -A:562
22H:22 -H:96
23H:145 -H:201
24L:22 -L:89
25L:135 -L:195

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Gln L:6 -Pro L:7
2Ala L:29 -Gly L:30
3Gly L:30 -Arg L:31
4Val L:95 -Pro L:96
5Tyr L:141 -Pro L:142
6Gly H:101 -Tyr H:102
7Phe H:151 -Pro H:152
8Glu H:153 -Pro H:154

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WSQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WSQ)

(-) Exons   (0, 0)

(no "Exon" information available for 3WSQ)

(-) 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:555
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..........hhhhhhhhhhhhh.....ee..eeee.........hhhhh......eeee...................hhhh.eeeee..........................eeee............hhhhhh........eee...............................................................hhhhh...................................................eee....ee.......eee.......eee.........ee...hhhhh........hhhhhh...eee..eee.......hhhhh..........hhhhh.ee...eee.................ee....hhhh.eeeeee..................eeeee...........hhhhh.......eeee..................hhhhh..............eee..eee...........eeee..eeee........................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wsq A   1 TQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLSPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVA 564
                                    10        20        30        40        50        60        70        80        90       100||     119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559     
                                                                                                                              101|                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                                                                                                                               111                                                                                                                                                                                                                                                                                                                                                                                                                                                                     


Chain H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh..eeee........eee...........hhhhh..eeee........eeee...hhhhheeeeee...............eeee........eeeee......ee..eeeeeeeeeee.......ee.hhh.....ee..........eee.eeeeee........eeee..........eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wsq H   1 EVQLVQSGGGLKVPGGSVKVSCKASSYTFTSYGISWVRQAPGQGLEWMGDVNTYAGNTNYAQKLQGRVTMTTDTGTSTAYMELRSLRSDDAAVYYCARDRGYYAFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        


Chain L from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee.....eeeeee...........eeeee......eeeee............ee......eeeeee........eeeeee............eeeee.......ee........hhhh.eeeeeeeee......eee..ee..ee....ee.............eeeeeeeeehhhhh...eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wsq L   1 QSVLTQPPSASGTPGQTVTLSCSGSRTNAGRDPVSWYQQLPGTAPKLLTSTAPQGPSGVPDRFSGSKSGTSSSLAISGLQSGDEADYYCTVWDSVPGASVFGSGTFLTVTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 3WSQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WSQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WSQ)

(-) Gene Ontology  (73, 73)

Asymmetric/Biological Unit(hide GO term definitions)

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Asymmetric/Biological Unit
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  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3wsq)
 
  Sites
(no "Sites" information available for 3wsq)
 
  Cis Peptide Bonds
    Ala L:29 - Gly L:30   [ RasMol ]  
    Gln L:6 - Pro L:7   [ RasMol ]  
    Glu H:153 - Pro H:154   [ RasMol ]  
    Gly H:101 - Tyr H:102   [ RasMol ]  
    Gly L:30 - Arg L:31   [ RasMol ]  
    Phe H:151 - Pro H:152   [ RasMol ]  
    Tyr L:141 - Pro L:142   [ RasMol ]  
    Val L:95 - Pro L:96   [ RasMol ]  
 

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 Databases and Analysis Tools

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  3wsq
    Family and Domain Information: ProDom | SYSTERS
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    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
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Access by UniProt ID/Accession number
  ERBB2_HUMAN | P04626
    Comparative Protein Structure Models: ModBase
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    Protein-protein Interaction: DIP
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  2.7.10.1
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  ERBB2_HUMAN | P04626
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 Related Entries

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

UniProtKB/Swiss-Prot
        ERBB2_HUMAN | P04626: 1mfg 1mfl 1mw4 1n8z 1ovc 1qr1 1s78 2a91 2jwa 2ks1 2l4k 2n2a 3be1 3h3b 3mzw 3n85 3pp0 3rcd 3wlw 4gfu 4hrl 4hrm 4hrn 4nnd 5k33 5kwg

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3WSQ)