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(-) Description

Title :  CRYSTAL STRUCTURE OF PANITUMUMAB IN COMPLEX WITH EPIDERMAL GROWTH FACTOR RECEPTOR DOMAIN 3 MUTANT S468R.
 
Authors :  E. A. Sickmier
Date :  09 Aug 16  (Deposition) - 05 Oct 16  (Release) - 05 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  H,J,K,L,M,N
Biol. Unit 1:  J,K,M  (1x)
Biol. Unit 2:  H,L,N  (1x)
Keywords :  Cetuximab, Panitumumab, Egfr, Vectibix, Erbitux, Transferase-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. A. Sickmier, R. J. Kurzeja, K. Michelsen, M. Vazir, E. Yang, A. S. Tasker
The Panitumumab Egfr Complex Reveals A Binding Mechanism That Overcomes Cetuximab Induced Resistance.
Plos One V. 11 63366 2016
PubMed-ID: 27658254  |  Reference-DOI: 10.1371/JOURNAL.PONE.0163366

(-) Compounds

Molecule 1 - PANITUMUMAB FAB LIGHT CHAIN
    Chains: K, L
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Taxid: 10029
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - PANITUMUMAB FAB HEAVY CHAIN
    Chains: J, H
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Taxid: 10029
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - EPIDERMAL GROWTH FACTOR RECEPTOR
    Chains: M, N
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 335-528
    Gene: EGFR, ERBB, ERBB1, HER1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTO-ONCOGENE C-ERBB-1,RECEPTOR TYROSINE-PROTEIN KINASE ERBB-1

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : HJKLMN
Biological Unit 1 (1x):  JK M 
Biological Unit 2 (1x): H  L N

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 22)

Asymmetric Unit (4, 22)
No.NameCountTypeFull Name
11PE3Ligand/IonPENTAETHYLENE GLYCOL
2EDO3Ligand/Ion1,2-ETHANEDIOL
3GOL4Ligand/IonGLYCEROL
4SO412Ligand/IonSULFATE ION
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2EDO2Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4SO43Ligand/IonSULFATE ION
Biological Unit 2 (4, 14)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4SO49Ligand/IonSULFATE ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS K:39 , LYS K:45binding site for residue SO4 K 301
02AC2SOFTWAREPRO K:59 , SER K:60binding site for residue SO4 K 302
03AC3SOFTWAREASP K:1 , GLN K:27 , HIS K:93 , ASN M:473binding site for residue SO4 K 303
04AC4SOFTWAREPRO K:8 , SER K:9binding site for residue GOL K 304
05AC5SOFTWARETHR K:20 , THR K:22 , SER L:7 , PRO L:8 , THR L:20 , THR L:22binding site for residue GOL K 305
06AC6SOFTWAREGLN K:38 , ALA K:84 , THR K:85 , GLU K:165 , HOH K:407binding site for residue EDO K 306
07AC7SOFTWAREILE J:94 , TYR J:96 , MET J:114 , GLY K:41 , LYS K:42binding site for residue 1PE J 301
08AC8SOFTWAREASN J:161 , SER J:162binding site for residue EDO J 302
09AC9SOFTWARELEU L:11 , SER L:12binding site for residue SO4 L 301
10AD1SOFTWAREGLN L:27 , ASP L:28binding site for residue SO4 L 302
11AD2SOFTWAREARG L:211binding site for residue SO4 L 303
12AD3SOFTWARELYS L:39 , LYS L:42 , LYS L:45binding site for residue SO4 L 304
13AD4SOFTWAREASP L:1 , GLN L:27 , HIS L:93 , ASN N:473binding site for residue SO4 L 305
14AD5SOFTWARESER L:9 , GLN L:38 , ALA L:84 , THR L:85 , GLY L:100 , GLY L:101 , LYS L:103 , GLU L:165binding site for residue 1PE L 306
15AD6SOFTWARESER L:9binding site for residue GOL L 307
16AD7SOFTWAREGLY H:124binding site for residue SO4 H 301
17AD8SOFTWAREASN H:161 , SER H:162 , ASN H:203 , HOH H:402 , ASP L:185binding site for residue SO4 H 302
18AD9SOFTWARESER H:121 , THR H:122binding site for residue SO4 H 303
19AE1SOFTWAREILE H:94 , TYR H:96 , GLN H:111 , GLY H:112 , GLU H:154 , HOH H:415 , GLN L:38 , LYS L:42binding site for residue 1PE H 304
20AE2SOFTWAREPRO H:9 , GLY H:10binding site for residue GOL H 305
21AE3SOFTWAREASP H:33 , GLN N:408 , VAL N:417binding site for residue EDO H 306
22AE4SOFTWAREHIS M:359 , SER N:474binding site for residue SO4 N 601

(-) SS Bonds  (14, 14)

Asymmetric Unit
No.Residues
1H:146 -H:202
2J:22 -J:97
3J:146 -J:202
4K:23 -K:88
5K:134 -K:194
6L:23 -L:88
7L:134 -L:194
8M:313 -M:338
9M:446 -M:475
10M:482 -M:491
11N:313 -N:338
12N:446 -N:475
13N:482 -N:491
14N:486 -N:499

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser K:7 -Pro K:8
2Leu K:94 -Pro K:95
3Tyr K:140 -Pro K:141
4Phe J:152 -Pro J:153
5Glu J:154 -Pro J:155
6Ser L:7 -Pro L:8
7Leu L:94 -Pro L:95
8Tyr L:140 -Pro L:141
9Phe H:152 -Pro H:153
10Glu H:154 -Pro H:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5SX5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5SX5)

(-) Exons   (0, 0)

(no "Exon" information available for 5SX5)

(-) 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 H from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee...ee.....eeeeee..........eeeeeeeee...eeeeeeee.....eee...hhh.eeeeee....eeeeee...hhhhheeeeeeeee....eeee...eeeee........eeeee.....eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee....eeeeeeehhhheeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5sx5 H    1 QVQLQESGPGLVKPSETLSLTCTVSGGSVSSGDYYWTWIRQSPGKGLEWIGHIYYSGNTNYNPSLKSRLTISIDTSKTQFSLKLSSVTAADTAIYYCVRDRVTGAFDIWGQGTMVTVSSASTKGPSVFPLAPCSTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSQTYTCNVDHKPSNTKVDKTVE  218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  146       156       166       176       186     ||201       211       
                                                                                                                                                               134|                                                192|                    
                                                                                                                                                                141                                                 198                    


Chain J from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeeeee...eeeeeeee.....eee...hhh.eeeeee....eeeeee...hhhhheeeeeeeee....eeee...eeeee........eeeee......eeeeeeeeee.....eeee........eee...ee.....eeeeeeeee...eeeeeeehhhheeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5sx5 J    1 QVQLQESGPGLVKPSETLSLTCTVSGGSVSSGDYYWTWIRQSPGKGLEWIGHIYYSGNTNYNPSLKSRLTISIDTSKTQFSLKLSSVTAADTAIYYCVRDRVTGAFDIWGQGTMVTVSSASTKGPSVFPLAPCSSTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPQTYTCNVDHKPSNTKVDKTVE  218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  145       155       165       175       185     ||201       211       
                                                                                                                                                               134|                                                191|                    
                                                                                                                                                                140                                                 198                    


Chain K from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5sx5 K    1 DIQMTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYFCQHFDHLPLAFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    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:212
                                                                                                                                                                                                                                                     
               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..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5sx5 L    1 DIQMTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYFCQHFDHLPLAFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  


Chain M from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                   
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...hhhhh........hhhhhh...eee..eee.hhhhhh.........hhhhhhhhhhh.ee...eee.........hhhhh...ee....hhhh.eeeeee.............ee...eeeee...........hhhhh.......eeee...hhhhhhhh................hhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5sx5 M  310 KKVCNGIGIGEFKDSLSIDATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLDITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIIRNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSHH 1503
                                   319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499 || 
                                                                                                                                                                                                                         501| 
                                                                                                                                                                                                                         1502 


Chain N from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee...hhhhh........hhhhhh...eee..eeehhhhhhhhhhhh....hhhhhhhhhhh.ee...eee.........hhhhh...ee....hhhh.eeeeee.............ee...eeeee...........hhhhh.......eeee...hhhhhhhh................hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5sx5 N  310 KKVCNGIGIGEFKDSLSIDATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLDITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIIRNRGENSCKATGQVCHALCSPEGCWGPEPRDCVS  501
                                   319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 5SX5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5SX5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5SX5)

(-) Gene Ontology  (111, 111)

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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 4uv7 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 5u8l 5ug8 5ug9 5uga 5ugb 5ugc

(-) Related Entries Specified in the PDB File

5sx4