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(-) Description

Title :  HIGH-AFFINITY AXL DECOY RECEPTOR
 
Authors :  I. I. Mathrews, S. Kapur, M. S. Kariolis, J. R. Cochran
Date :  24 May 17  (Deposition) - 21 Jun 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Engineered Decoy Receptor, Human Cancers, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. S. Kariolis, Y. R. Miao, A. Diep, S. E. Nash, M. M. Olcina, D. Jiang, D. S. Jones, S. Kapur, I. I. Mathews, A. C. Koong, E. B. Rankin, J. R. Cochran, A. J. Giaccia
Inhibition Of The Gas6/Axl Pathway Augments The Efficacy Of Chemotherapies.
J. Clin. Invest. V. 127 183 2017
PubMed-ID: 27893463  |  Reference-DOI: 10.1172/JCI85610

(-) Compounds

Molecule 1 - GROWTH ARREST-SPECIFIC PROTEIN 6
    Chains: A, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: RESIDUES 324-718
    Gene: GAS6, AXLLG
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GAS-6,AXL RECEPTOR TYROSINE KINASE LIGAND
 
Molecule 2 - TYROSINE-PROTEIN KINASE RECEPTOR UFO
    Chains: C, D
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Fragment: RESIDUES 34-135
    Gene: AXL, UFO
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AXL ONCOGENE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2CL2Ligand/IonCHLORIDE ION
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:329 , GLU A:331 , ARG A:440 , ASP A:656 , HOH A:809 , HOH A:822binding site for residue CA A 703
2AC2SOFTWAREVAL A:292binding site for residue CL A 704
3AC3SOFTWAREASP B:329 , GLU B:331 , ARG B:440 , ASP B:656 , HOH B:843 , HOH B:847binding site for residue CA B 703
4AC4SOFTWARESER B:291 , VAL B:292binding site for residue CL B 704
5AC5SOFTWAREARG A:310 , GLY A:339 , HIS A:418 , ASN A:420binding site for Poly-Saccharide residues NAG A 701 through NAG A 702 bound to ASN A 420
6AC6SOFTWAREARG B:310 , GLY B:339 , HIS B:340 , HIS B:418 , ASN B:420 , HOH B:824 , GLU D:59binding site for Poly-Saccharide residues NAG B 701 through NAG B 702 bound to ASN B 420

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:283 -A:570
2A:444 -A:470
3A:643 -A:670
4B:283 -B:570
5B:444 -B:470
6B:643 -B:670
7C:49 -C:110
8D:49 -D:110

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5VXZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VXZ)

(-) 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 A from PDB  Type:PROTEIN  Length:376
                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............ee..........eeeeeee......eeeeeeee....eeeeeee......eeeeeee..eeeeeeee..eeeeeee.........eeeeeeee..eeeeee..eeeeeee......eee..eeeeeeee.....hhhhh.........eeeeeeee.....hhhhhhhhhhhhhh........eee.....eee........eeeeeeeee....eeeeeeee....eeeeeeeee..eeeeee..eeeeeee.hhhhh..eeeeeeee..eeeeee..ee.ee..hhhhhhhhhhhhhhhhh...eeee......hhhhh.......eeeeeee..ee.hhhhh.ee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vxz A 281 LPCVPFSVAKSVKSLYLGRMFSGTPVIRLRFKRLQPTRLVAEFDFRTFDPEGILLFAGGHQDSTWIVLALRAGRLELQLRYNGVGRVTSSGPVINHGMWQTISVEELARNLVIKVNRDAVMKIAVAGDLFQPERGLYHLNLTVGGIPFHEKDLVQPINPRLDGCMRSWNWLNGEDTTIQETVKVNTRMQCFSVTERGSFYPGSGFAFYSLDYMTWEVEVVAHIRPAADTGVLFALWAPDLRAVPLSVALVDQLVVLAVEHTALALMEIKVCDGQEHVVTVSLRDGEATLEVDGTRGQSEVSAAQLQERLAVLERHLRSPVLTFAGGLPDVPVTSAPVTAFYRGCMTLEVNRRLLDLDEAAYKHSDITAHSCPPVEP 675
                                   290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490  ||   510       520       530       540||     559       569       579       589       599       609       619       629       639       649       659       669      
                                                                                                                                                                                                                                              493|                                  541|                                                                                                                            
                                                                                                                                                                                                                                               504                                   551                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:376
                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............ee..........eeeeeee......eeeeeeee....eeeeeee......eeeeeee..eeeeeeee..eeeeeee.........eeeeeeee..eeeeee..eeeeeee......eee..eeeeeeee.....hhhhh.........eeeeeeee.....hhhhhhhhhhhhhh........eee.....eee........eeeeeeeee....eeeeeeee....eeeeeeeee..eeeeee..eeeeeee........eeeeeeee..eeeeee..ee.ee..hhhhhhhhhhhhhhhh....eeee..................eeeeeee..ee.hhhhh.ee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vxz B 281 LPCVPFSVAKSVKSLYLGRMFSGTPVIRLRFKRLQPTRLVAEFDFRTFDPEGILLFAGGHQDSTWIVLALRAGRLELQLRYNGVGRVTSSGPVINHGMWQTISVEELARNLVIKVNRDAVMKIAVAGDLFQPERGLYHLNLTVGGIPFHEKDLVQPINPRLDGCMRSWNWLNGEDTTIQETVKVNTRMQCFSVTERGSFYPGSGFAFYSLDYMTWEVEVVAHIRPAADTGVLFALWAPDLRAVPLSVALVDQLVVLAVEHTALALMEIKVCDGQEHVVTVSLRDGEATLEVDGTRGQSEVSAAQLQERLAVLERHLRSPVLTFAGGLPDVPVTSAPVTAFYRGCMTLEVNRRLLDLDEAAYKHSDITAHSCPPVEP 675
                                   290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490  ||   510       520       530       540||     559       569       579       589       599       609       619       629       639       649       659       669      
                                                                                                                                                                                                                                              493|                                  541|                                                                                                                            
                                                                                                                                                                                                                                               504                                   551                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:102
                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee....ee......eeeeeeeeee......eeee..ee....eeeeeeee.......eeeeeeeeee...hhhhheeeeeeeee..eeee...eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 5vxz C  27 ESPFVSNPGNITGARGLTGTLRCQLQVQGEPPEVHWLRDGQILELVDSTQTQVPLGEDEQGDWIVASQLRITSLQLSDTGQYQCLVFLGHQTFVSQPGYVRL 128
                                    36        46        56        66        76        86        96       106       116       126  


Chain D from PDB  Type:PROTEIN  Length:102
                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee....ee......eeeeeeeeee......eeee..ee.....eeeeeee.......eeeeeeeeee...hhhhheeeeeeeee..eeee...eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 5vxz D  27 ESPFVSNPGNITGARGLTGTLRCQLQVQGEPPEVHWLRDGQILELVDSTQTQVPLGEDEQGDWIVASQLRITSLQLSDTGQYQCLVFLGHQTFVSQPGYVRL 128
                                    36        46        56        66        76        86        96       106       116       126
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (129, 153)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        GAS6_HUMAN | Q14393: 1h30 2c5d 4ra0
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(-) Related Entries Specified in the PDB File

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