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(-) Description

Title :  NANOBODY/VHH DOMAIN 9G8 IN COMPLEX WITH THE EXTRACELLULAR REGION OF EGFR
 
Authors :  K. M. Ferguson, K. R. Schmitz
Date :  16 May 13  (Deposition) - 28 Aug 13  (Release) - 28 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.82
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Cell Surface Receptor, Glycoprotein, Nanobody, Vhh Domain, Camelid Vh Domain, Antibody, Antigen, Antibody Complex, Transferase-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. R. Schmitz, A. Bagchi, R. C. Roovers, P. M. P. Van Bergen En Henegouwen, K. M. Ferguson
Structural Evaluation Of Egfr Inhibition Mechanisms For Nanobodies/Vhh Domains.
Structure V. 21 1214 2013
PubMed-ID: 23791944  |  Reference-DOI: 10.1016/J.STR.2013.05.008

(-) Compounds

Molecule 1 - EPIDERMAL GROWTH FACTOR RECEPTOR
    Chains: A
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFASTBAC
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: EXTRACELLULAR REGION (UNP RESIDUES 25-642)
    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
 
Molecule 2 - CETUXIMAB LIGHT CHAIN
    Chains: C
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Common: MOUSE
    Expression System Plasmid: PDHL2
    Expression System Strain: SP2/0-AG15
    Expression System Taxid: 10090
    Expression System Vector Type: PLASMID
    Fragment: FAB
    Organism Common: MOUSE, HUMAN
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606
 
Molecule 3 - CETUXIMAB HEAVY CHAIN
    Chains: D
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Common: MOUSE
    Expression System Plasmid: PDHL2
    Expression System Strain: SP2/0-AG15
    Expression System Taxid: 10090
    Expression System Vector Type: PLASMID
    Fragment: FAB
    Organism Common: MOUSE, HUMAN
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606
 
Molecule 4 - NANOBODY/VHH DOMAIN 9G8
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: LLAMA
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:320 , SER A:324 , LEU A:325 , SER A:326 , ASN A:328 , ASN A:331 , VAL A:350 , THR A:358 , THR A:360BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 328 RESIDUES 701 TO 702
2AC2SOFTWARELYS A:336 , ASN A:337BINDING SITE FOR MONO-SACCHARIDE NAG A 703 BOUND TO ASN A 337
3AC3SOFTWAREASN A:389BINDING SITE FOR MONO-SACCHARIDE NAG A 704 BOUND TO ASN A 389
4AC4SOFTWAREGLU A:388 , ASN A:389 , ASN A:420 , THR A:422 , ASN A:444BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 420 RESIDUES 705 TO 706
5AC5SOFTWAREASN A:504 , ASP A:513BINDING SITE FOR MONO-SACCHARIDE NAG A 707 BOUND TO ASN A 504
6AC6SOFTWAREASN D:88BINDING SITE FOR MONO-SACCHARIDE NAG D 301 BOUND TO ASN D 88

(-) SS Bonds  (25, 25)

Asymmetric/Biological Unit
No.Residues
1A:7 -A:34
2A:208 -A:216
3A:212 -A:224
4A:227 -A:236
5A:240 -A:267
6A:271 -A:283
7A:287 -A:302
8A:305 -A:309
9A:313 -A:338
10A:446 -A:475
11A:482 -A:491
12A:486 -A:499
13A:502 -A:511
14A:515 -A:531
15A:534 -A:547
16A:538 -A:555
17A:558 -A:567
18A:571 -A:593
19A:596 -A:604
20A:600 -A:612
21B:22 -B:96
22C:23 -C:88
23C:134 -C:194
24D:22 -D:95
25D:146 -D:202

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Glu A:521 -Pro A:522
2Ser B:54 -Ser B:55
3Ser C:7 -Pro C:8
4Trp C:94 -Pro C:95
5Tyr C:140 -Pro C:141
6Phe D:152 -Pro D:153
7Glu D:154 -Pro D:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KRP)

(-) 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:534
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee...........hhhhhhhhhhhhhh...ee...eeee.......hhhhhh..ee...eeee.............ee.........eeeeee...................ee...eeeee.........................................eee......eee.....eee..eee.......ee.....ee......eeeeee..eeeeee.......eee...hhhhh.......hhhhhhh...eee..eee.hhhhhhhhhhh....hhhhhhhhhhh.ee...eee.........hhhhh...ee....hhhh.eeeeee.............ee...eeeee...........hhhhh.......eeee...hhhhhhhh................hhhhh.....ee....ee...........eee....eee...........................ee....ee........hhhhh...eeee...eeee............hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4krp A   4 KKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIRGNMYYENSYALAVLSNYDANKTGLKELPMRNLQEILHGAVRFSNNPALCHNQCAAGCTGPRESDCLVCRKFRDEATCKDTCPPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYVVTDHGSCVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCNLLEGEPREFVENSECIQCHPECLPQAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVMGENNTLVWKYADAGHVCHLCHPNCTYGCTGPGLEGC 612
                                    13        23        33        43        53        63        73        83        93       103       113       123       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608    
                                                                                                                                                          132|                                                                                                                                                                                                                                                                                                                                                                                                                    
                                                                                                                                                           208                                                                                                                                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:116
                                                                                                                                                    
               SCOP domains d4krpb_ B: automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....eeeee......eeeeeeee.....eeeeeeee.....eee........eeeee....eeeee....hhhhheeeeeeeee.......hhhhh...ee...eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 4krp B   1 EVQLVESGGGLLSCAASGRTFSSYAMGWFRQAPGKEREFVVAINWSSGSTYYADSVKGRFTISRDNAKNTMYLQMNSLKPEDTAVYYCAAGYQINSGNYNFKDYEYDYWGQGTQVT 124
                                    10||      28        38        48        58        68        78        88        98       108       118      
                                     11|                                                                                                        
                                      20                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains d4krpc1 C:1-107 automated matches                                                                          d4krpc2 C:108-211 automated matches                                                                      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.eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4krp C   1 DILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 


Chain D from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee.....eeeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee......eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee..........eeeeeehhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4krp D   1 QVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSKTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVE 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    || 145       155       165       175       185       195       205       215   
                                                                                                                                                                135|                                                                             
                                                                                                                                                                 141
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (111, 111)

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
        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 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 5sx5 5u8l 5ug8 5ug9 5uga 5ugb 5ugc

(-) Related Entries Specified in the PDB File

4krl 4krm 4krn 4kro