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(-) Description

Title :  NANOBODY/VHH DOMAIN 7D12 IN COMPLEX WITH DOMAIN III OF THE EXTRACELLULAR REGION OF EGFR, PH 6.0
 
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 :  2.85
Chains :  Asym./Biol. Unit :  A,B
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 - NANOBODY/VHH DOMAIN 7D12
    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
 
Molecule 2 - 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 DOMAIN III (UNP RESIDUES 335-538)
    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

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1IOD1Ligand/IonIODIDE ION
2MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:57 , ALA B:103 , TRP B:104BINDING SITE FOR RESIDUE MES B 201
2AC2SOFTWARELYS A:430 , LYS A:455 , PHE A:457 , GLU A:489 , CYS A:502 , ARG A:503 , HOH A:705BINDING SITE FOR RESIDUE MES A 606
3AC3SOFTWARESER A:324 , LEU A:325 , SER A:326 , ASN A:328 , ASN A:331 , ASP A:355 , THR A:358 , THR A:360 , HOH A:718BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 328 RESIDUES 601 TO 602
4AC4SOFTWARELYS A:336 , ASN A:337BINDING SITE FOR MONO-SACCHARIDE NAG A 603 BOUND TO ASN A 337
5AC5SOFTWARETRP A:386 , ASN A:420 , TYR B:109BINDING SITE FOR MONO-SACCHARIDE NAG A 604 BOUND TO ASN A 420

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:313 -A:338
2A:446 -A:475
3A:482 -A:491
4A:486 -A:499
5A:502 -A:511
6B:22 -B:96

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4KRL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KRL)

(-) 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:205
                                                                                                                                                                                                                                             
               SCOP domains d4krla1 A:307-480 automated matches                                                                                                                                           d4krla2 A:481-511               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...hhhhh.......hhhhhhh...eee..eee.hhhhhh.........hhhhhhhhhhh.ee...eee.........hhhhh...ee....hhhh.eeeeee.............ee...eeeee......hhhhhhhhhh.......eeee...hhhhhhhh................hhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4krl A 307 LEEKKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSCRNVSRGREC 511
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506     


Chain B from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains d4krlb_ B: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..ee.......eeeeeeee.....eeeeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee......hhhhh.ee...eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4krl B   1 QVKLEESGGGSVQTGGSLRLTCAASGRTSRSYGMGWFRQAPGKEREFVSGISWRGDSTGYADSVKGRFTISRDNAKNTVDLQMNSLKPEDTAIYYCAAAAGSAWYGTLYEYDYWGQGTQVTV 122
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (111, 111)

Asymmetric/Biological Unit(hide GO term definitions)

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  4krl
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  EGFR_HUMAN | P00533
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  2.7.10.1
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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 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 5sx5 5u8l 5ug8 5ug9 5uga 5ugb 5ugc

(-) Related Entries Specified in the PDB File

4krm 4krn 4kro 4krp