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(-) Description

Title :  CRYSTAL STRUCTURE OF KIT D4D5 FRAGMENT IN COMPLEX WITH ANTI-KIT ANTIBODY FAB19
 
Authors :  A. V. Resheynyak, T. J. Boggon, I. Lax, J. Schlessinger
Date :  19 Apr 13  (Deposition) - 16 Oct 13  (Release) - 09 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  C,H,L
Keywords :  Receptor Tyrosine Kinase (Rtk), Fab, Ig Sf, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. V. Reshetnyak, B. Nelson, X. Shi, T. J. Boggon, A. Pavlenco, E. M. Mandel-Bausch, F. Tome, Y. Suzuki, S. S. Sidhu, I. Lax, J. Schlessinger
Structural Basis For Kit Receptor Tyrosine Kinase Inhibitio By Antibodies Targeting The D4 Membrane-Proximal Region.
Proc. Natl. Acad. Sci. Usa V. 110 17832 2013
PubMed-ID: 24127596  |  Reference-DOI: 10.1073/PNAS.1317118110

(-) Compounds

Molecule 1 - FAB19 HEAVY CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PHAGEMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB19 LIGHT CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PHAGEMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - MAST/STEM CELL GROWTH FACTOR RECEPTOR KIT
    Chains: C
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: UNIDENTIFIED BACULOVIRUS
    Expression System Plasmid: PFASTBAC
    Expression System Taxid: 10469
    Expression System Vector Type: BACMID
    Gene: KIT, SCFR
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SCFR, PIEBALD TRAIT PROTEIN, PBT, PROTO-ONCOGENE C-KIT, TYROSINE-PROTEIN KINASE KIT, P145 C-KIT, V-KIT HARDY-ZUCKERMAN 4 FELINE SARCOMA VIRAL ONCOGENE HOMOLOG

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : CHL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN C:320 , LEU C:416 , THR C:417 , TYR C:418 , SER H:30 , TYR H:54 , THR H:74BINDING SITE FOR MONO-SACCHARIDE NAG C 601 BOUND TO ASN C 320

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1C:428 -C:491
2C:443 -C:450
3H:22 -H:96
4H:144 -H:200
5L:23 -L:88
6L:135 -L:195

(-) Cis Peptide Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Ser L:67 -Gly L:68
3Tyr L:141 -Pro L:142
4Ser L:157 -Gly L:158
5Phe H:150 -Pro H:151
6Glu H:152 -Pro H:153
7Phe C:340 -Pro C:341
8Phe C:433 -Pro C:434
9Leu C:455 -Pro C:456
10Gly C:466 -Pro C:467
11Pro C:467 -Pro C:468

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K94)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K94)

(-) Exons   (0, 0)

(no "Exon" information available for 4K94)

(-) 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 C from PDB  Type:PROTEIN  Length:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeee.....eeeeeeeeee...eeeeeee..ee....eeeee........eeeeeeee...hhhhheeeeeeee....eeeeeeeeee.eeeeeeeeee....eeeeeeeee...eeeeeeee...........eeeee.......eeeeeeee.......eeeeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k94 C 310 KGFINIFPMINTTVFVNDGENVDLIVEYEAFPKPEHQQWIYMNRTFTDKWEDYPKSENESNIRYVSELHLTRLKGTEGGTYTFLVSNSDVNAAIAFNVYVNTKPEILTYDRLVNGMLQCVAAGFPEPTIDWYFCPGTRCSASVLPVDVQTLNGPPFGKLVVQSSIDSSAFKHNGTVECKAYNDVGKTSAYFNFAF 508
                                   319       329       339       349       359       369       379       389       399       409       419       429       439      |451       461 ||    473       483       493       503     
                                                                                                                                                                  446|           463|                                          
                                                                                                                                                                   449            466                                          


Chain H from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeee..eeeee...eeeee........eeeee...eeeeeee.....eeee.hhh.....ee...ee.....eeeeee.........eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k94 H   1 EVQLVESGGGLVQPGGSLRLSCAASGFNISSYSMHWVRQAPGKGLEWVASIYPYSGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARYVYHALDYWGQGTLVTVSSASTKGPSVFPLAPLGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSTYICNVNHKPSNTKVDKKVEP 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130|      151       161       171       181       191||     205       215  
                                                                                                                                                           130|                                               192|                    
                                                                                                                                                            142                                                197                    


Chain L from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains d4k94l1 L:3-108 automated matches                                                                         d4k94l2 L:109-212 automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee..eeee.....eeeeee........eeeeee......eeeee...ee.......eeeee....eeeee...hhhhheeeeeeeee...eeee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee...ee...eeeee.........eeeeeeeeeehhhhh....eeeeee.......eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4k94 L   3 QMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQWAVHSLITFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 212
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K94)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K94)

(-) Gene Ontology  (104, 104)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu H:152 - Pro H:153   [ RasMol ]  
    Gly C:466 - Pro C:467   [ RasMol ]  
    Leu C:455 - Pro C:456   [ RasMol ]  
    Phe C:340 - Pro C:341   [ RasMol ]  
    Phe C:433 - Pro C:434   [ RasMol ]  
    Phe H:150 - Pro H:151   [ RasMol ]  
    Pro C:467 - Pro C:468   [ RasMol ]  
    Ser L:157 - Gly L:158   [ RasMol ]  
    Ser L:67 - Gly L:68   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Tyr L:141 - Pro L:142   [ RasMol ]  
 

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  4k94
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  KIT_HUMAN | P10721
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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
        KIT_HUMAN | P10721: 1pkg 1qzj 1qzk 1r01 1t45 1t46 2e9w 2ec8 2iuh 2vif 3g0e 3g0f 4hvs 4k9e 4pgz 4u0i

(-) Related Entries Specified in the PDB File

4k9e