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(-) Description

Title :  CRYSTAL STRUCTURE OF KIT D4D5 FRAGMENT IN COMPLEX WITH ANTI-KIT ANTIBODIES FAB79D
 
Authors :  A. V. Resheynyak, T. J. Boggon, I. Lax, J. Schlessinger
Date :  19 Apr 13  (Deposition) - 16 Oct 13  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  C,H,L
Keywords :  Receptor Tyrosine Kinase (Rtk), Igg, Fab, 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 - LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
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 Taxid: 10469
    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 , THR C:322 , PHE C:324 , 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:90
6L:137 -L:197

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Ile L:2 -Gln L:3
2Ser L:7 -Pro L:8
3Ser L:26 -Gln L:27
4Tyr L:143 -Pro L:144
5Phe H:150 -Pro H:151
6Glu H:152 -Pro H:153
7Phe C:340 -Pro C:341
8Phe C:433 -Pro C:434
9His C:485 -Asn C:486

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K9E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K9E)

(-) Exons   (0, 0)

(no "Exon" information available for 4K9E)

(-) 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:193
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee....eeeeeeeeee....eeeeee..ee....eeeee........eeeeeeee........eeeeeeee....eeeeeeeeeeeeeeeeeeeee.....eeeeeeee...eeeeeee...........eeeee......eeeeeee.........eeeeeee....eeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k9e C 311 GFINIFPMINTTVFVNDGENVDLIVEYEAFPKPEHQQWIYMNRTFTDKWEDYPKSENESNIRYVSELHLTRLKGTEGGTYTFLVSNSDVNAAIAFNVYVNTKPEILTYDRLVNGMLQCVAAGFPEPTIDWYFCPQRCSASVLPVDVQTLNSSFGKLVVQSSIDSSAFKHNGTVECKAYNDVGKTSAYFNFAFK 509
                                   320       330       340       350       360       370       380       390       400       410       420       430       440   ||  453       463 ||    476       486       496       506   
                                                                                                                                                               444|              465|                                        
                                                                                                                                                                448               469                                        


Chain H from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...ee.....eeeeeeee.......eeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeee..eeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k9e H   0 SEVQLVESGGGLVQPGGSLRLSCAASGFNISVYMMHWVRQAPGKGLEWVASIYPYSGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARYVYHALDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS 219
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219


Chain L from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains d4k9el1 L:2-110 automated matches                                                                            d4k9el2 L:111-227 automated matches                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee....eeeeeeee........eeeeeee......eeeee...ee.......eeeee....eeeeee..hhhhh.eeeeeeee...eeee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k9e L   2 IQMTQSPSSLSASVGDRVTITCRASQRGLRNVAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQWAVHSLITFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEYKDDDD 227
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211    || 226 
                                                                                                                                                                                                                                                216|     
                                                                                                                                                                                                                                                 222
   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  (2, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K9E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K9E)

(-) 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 ]  
    His C:485 - Asn C:486   [ RasMol ]  
    Ile L:2 - Gln L:3   [ RasMol ]  
    Phe C:340 - Pro C:341   [ RasMol ]  
    Phe C:433 - Pro C:434   [ RasMol ]  
    Phe H:150 - Pro H:151   [ RasMol ]  
    Ser L:26 - Gln L:27   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Tyr L:143 - Pro L:144   [ RasMol ]  
 

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  4k9e
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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 4k94 4pgz 4u0i

(-) Related Entries Specified in the PDB File

4k94