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(-) Description

Title :  THE COMPLEX STRUCTURE OF EXTRACELLULAR DOMAIN OF EGFR AND GC1118A
 
Authors :  J. H. Yoo, H. S. Cho
Date :  05 Aug 14  (Deposition) - 14 Oct 15  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Transferase, Receptor Tyrosine Kinase, Antibody (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Lim, J. Yoo, M. S. Kim, M. Hur, E. H. Lee, H. S. Hur, J. C. Lee, S. N. Lee, T. W. Park, K. Lee, K. H. Chang, K. Kim, Y. Kang, K. W. Hong, S. H. Kim, Y. G. Kim, Y. Yoon, D. H. Nam, H. Yang, D. G. Kim, H. S. Cho, J. Won
Gc1118, An Anti-Egfr Antibody With A Distinct Binding Epitope And Superior Inhibitory Activity Against High- Affinity Egfr Ligands.
Mol. Cancer Ther. V. 15 251 2016
PubMed-ID: 26586721  |  Reference-DOI: 10.1158/1535-7163.MCT-15-0679

(-) Compounds

Molecule 1 - EPIDERMAL GROWTH FACTOR RECEPTOR
    Chains: A
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: EXTRACELLULAR DOMAIN, UNP RESIDUES 25-645
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTO-ONCOGENE C-ERBB-1, RECEPTOR TYROSINE-PROTEIN KINASE ERBB-1, EPIDERMAL GROWTH FACTOR RECEPTOR 1
 
Molecule 2 - GC1118A
    Chains: H
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHO
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - GC1118A
    Chains: L
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHO
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Organism Common: HUMAN
    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  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:321 , ASP A:323 , SER A:324 , LEU A:325 , SER A:326 , ASN A:328 , ASN A:331 , HOH A:2038 , HOH A:2055 , HOH A:2155BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A3281 THROUGH BMA A3283 BOUND TO ASN A 328
2AC2SOFTWAREASP A:290 , LYS A:336 , ASN A:337BINDING SITE FOR MONO-SACCHARIDE NAG A3371 BOUND TO ASN A 337
3AC3SOFTWAREGLU A:388 , ASN A:389 , ASN A:420 , ASN A:444 , HOH A:2083BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A4201 THROUGH NAG A4202 BOUND TO ASN A 420
4AC4SOFTWAREASN A:504 , VAL A:505 , VAL A:526 , ASP L:28 , THR L:74 , HOH L:2044BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A5441 THROUGH NAG A5442 BOUND TO ASN A 504

(-) SS Bonds  (28, 28)

Asymmetric/Biological Unit
No.Residues
1A:7 -A:34
2A:166 -A:175
3A:170 -A:183
4A:191 -A:199
5A:195 -A:207
6A:208 -A:216
7A:212 -A:224
8A:227 -A:236
9A:240 -A:267
10A:271 -A:283
11A:287 -A:302
12A:305 -A:309
13A:313 -A:338
14A:446 -A:475
15A:482 -A:491
16A:486 -A:499
17A:502 -A:511
18A:515 -A:531
19A:534 -A:547
20A:538 -A:555
21A:558 -A:567
22A:571 -A:593
23A:596 -A:604
24A:600 -A:612
25H:22 -H:96
26H:149 -H:205
27L:23 -L:93
28L:139 -L:199

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Arg A:273 -Asn A:274
2Glu A:296 -Asp A:297
3Glu A:521 -Pro A:522
4Gly H:142 -Gly H:143
5Phe H:155 -Pro H:156
6Glu H:157 -Pro H:158
7Thr L:7 -Pro L:8
8Trp L:99 -Pro L:100
9Tyr L:145 -Pro L:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UV7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UV7)

(-) Exons   (0, 0)

(no "Exon" information available for 4UV7)

(-) 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:596
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee...........hhhhhhhhhhhhhh...ee...eeee.......hhhhhhh.ee...eeee.............ee.........eeeeee...................ee...eeeee......hhhhhhhhhh.........hhhhh............................hhhh.......................eee..eee......eeee....eeee.....eee..eee.......ee.....ee......eeeee....eeeee.......eee...hhhhh........hhhhhh...eee..eeehhhhhhh.hhhh....hhhhhhhhhhh.ee...eee.........hhhhh...ee.........eeeeee.............ee...eeeee......hhhhhhhhhh.......eeee...hhhhhhhh...........................ee..ee............eeee..eeee...........................eee..eee....eeee.....eeeeee.....eee............hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uv7 A   1 LEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIRGNMYYENSYALAVLSNYDANKTGLKELPMRNLQEILHGAVRFSNNPALCNVESIQWRDIVSSQKCDPSCPNGSCWGAGEENCQKLTKIICAQQCSGRCRGKSPSDCCHNQCAAGCTGPRESDCLVCRKFRDEATCKDTCPPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYVVTDHGSCVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCNLLEGEPREFVENSECIQCHPECLPQAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVMGENNTLVWKYADAGHVCHLCHPNCTYGCTGPGLEGCP 613
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     ||167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607      
                                                                                                                                                                           146|                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                                                                                                                                                                            164                                                                                                                                                                                                                                                                                                                                                                                                                                                                 


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.eeeeee.....eeeeeee......eee.hhh...eeeeeehhh.eeeeee...hhhhheeeeeee..hhhhh..........eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uv7 H   1 EVQLVESGGGVVQPGGSLRLSCAASGFTFSDYDMSWIRQAPGKGLEWVSGILGGSERSYYRDSVKGRFTISRDNSRKTLYLQMNSLRAEDTAVYYCARHGSPGYTLYAWDYWGQGTTVTVSSASTKGPSVFPLAPSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPK 223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     ||145       155       165       175       185       195       205       215        
                                                                                                                                                                 136|                                                                                 
                                                                                                                                                                  142                                                                                 


Chain L from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               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..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4uv7 L   1 DIVMTQTPLSLPVTPGEPASISCRSNQDLTHSNGNTYLEWYLQKPGQSPRLLIYKVSNRFSGVPDRFSGSGAGTDFTLRISRVEAEDVGVYYCMQGTHWPWTFGQGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALNSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 216
                                    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 4UV7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UV7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UV7)

(-) Gene Ontology  (111, 111)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Glu H:157 - Pro H:158   [ RasMol ]  
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    Thr L:7 - Pro L:8   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        EGFR_HUMAN | P00533: 1dnq 1dnr 1ivo 1m14 1m17 1mox 1nql 1xkk 1yy9 1z9i 2eb2 2eb3 2exp 2exq 2gs2 2gs6 2gs7 2itn 2ito 2itp 2itq 2itt 2itu 2itv 2itw 2itx 2ity 2itz 2j5e 2j5f 2j6m 2jit 2jiu 2jiv 2ks1 2m0b 2m20 2n5s 2rf9 2rfd 2rfe 2rgp 3b2u 3b2v 3bel 3buo 3c09 3g5v 3g5y 3gop 3gt8 3ika 3lzb 3njp 3ob2 3op0 3p0y 3pfv 3poz 3qwq 3ug1 3ug2 3vjn 3vjo 3vrp 3vrr 3w2o 3w2p 3w2q 3w2r 3w2s 3w32 3w33 4g5j 4g5p 4hjo 4i1z 4i20 4i21 4i22 4i23 4i24 4jq7 4jq8 4jr3 4jrv 4krl 4krm 4kro 4krp 4li5 4ll0 4lqm 4lrm 4r3p 4r3r 4r5s 4riw 4rix 4riy 4rj4 4rj5 4rj6 4rj7 4rj8 4tks 4uip 4wd5 4wkq 4wrg 4zau 4zjv 4zse 5c8k 5c8m 5c8n 5cal 5can 5cao 5cap 5caq 5cas 5cau 5cav 5cnn 5cno 5czh 5czi 5d41 5edp 5edq 5edr 5em5 5em6 5em7 5em8 5fed 5fee 5feq 5gmp 5gnk 5hcx 5hcy 5hcz 5hg5 5hg7 5hg8 5hg9 5hib 5hic 5j9y 5j9z 5jeb 5lv6 5sx4 5sx5 5u8l 5ug8 5ug9 5uga 5ugb 5ugc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4UV7)