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(-) Description

Title :  STRUCTURE OF THE HUMAN EPHA3 RECEPTOR LIGAND BINDING DOMAIN COMPLEXED WITH EPHRIN-A5
 
Authors :  G. J. Forse, A. R. Kolatkar, P. Kuhn
Date :  31 May 13  (Deposition) - 11 Jun 14  (Release) - 01 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Sandwich, Receptor Tyrosine Kinase, Ephrin Binding, Transferase- Transferase Receptor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. J. Forse, M. L. Uson, F. Nasertorabi, A. Kolatkar, I. Lamberto, E. B. Pasquale, P. Kuhn
Distinctive Structure Of The Epha3/Ephrin-A5 Complex Reveal A Dual Mode Of Eph Receptor Interaction For Ephrin-A5.
Plos One V. 10 27081 2015
PubMed-ID: 25993310  |  Reference-DOI: 10.1371/JOURNAL.PONE.0127081

(-) Compounds

Molecule 1 - EPHRIN TYPE-A RECEPTOR 3
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: LIGAND BINDING DOMAIN (UNP RESIDUES 29-201)
    Gene: EPHA3, EPHA3_HUMAN, ETK, ETK1, HEK, TYRO4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: EPH-LIKE KINASE 4, EK4, HEK4, HEK, HUMAN EMBRYO KINASE, TYROSINE-PROTEIN KINASE TYRO4, TYROSINE-PROTEIN KINASE RECEPTOR ETK1, EPH-LIKE TYROSINE KINASE 1
 
Molecule 2 - EPHRIN-A5
    Chains: B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Plasmid: PFASTBAC
    Expression System Taxid: 7111
    Expression System Vector Type: BACMID
    Fragment: RECEPTOR BINDING DOMAIN (UNP RESIDUES 27-166)
    Gene: EFNA5, EFNA5_HUMAN, EPLG7, LERK7
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AL-1, EPH-RELATED RECEPTOR TYROSINE KINASE LIGAND 7, LERK-7

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO45Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:136 , GLU A:137 , HIS A:138BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWARETYR A:96 , LYS A:200 , HOH A:410 , ARG B:104 , SER B:107 , PRO B:108BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWARELYS A:201 , HIS B:49 , ASP B:51 , HOH B:337BINDING SITE FOR RESIDUE CA B 203
4AC4SOFTWAREGLN A:93 , LYS A:94 , ARG B:159 , SER B:163 , HOH B:339BINDING SITE FOR RESIDUE SO4 B 204
5AC5SOFTWAREHOH A:422 , VAL B:78 , TYR B:80 , LYS B:98 , ARG B:131 , ARG B:134 , HOH B:332BINDING SITE FOR RESIDUE SO4 B 205
6AC6SOFTWARETHR A:37 , ILE A:38 , LYS A:94 , GLU A:170 , ARG B:104 , ASN B:162 , HOH B:308BINDING SITE FOR RESIDUE SO4 B 206
7AC7SOFTWARETYR B:35 , ASN B:37 , ASN B:40 , PRO B:63 , HIS B:64 , TYR B:65 , HOH B:307 , HOH B:311BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 37 RESIDUES 201 TO 202

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:71 -A:189
2A:106 -A:116
3B:53 -B:164
4B:62 -B:102
5B:90 -B:151

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:47 -Pro A:48
2Ile B:143 -Pro B:144

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L0P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L0P)

(-) Exons   (0, 0)

(no "Exon" information available for 4L0P)

(-) 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:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..........eee.....eeeeee.....eeeeeeee........eeee...ee.......eeeeeeee.hhhhh.........eeeeeeeee........hhhhheeeeeee.....hhhhhhhh....eeeeee.......eeeeeeee...eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l0p A  27 SGEVNLLDSKTIQGELGWISYPSHGWEEISGVDEHYTPIRTYQVCNVMDHSQNNWLRTNWVPRNSAQKIYVELKFTLRDCNSIPLVLGTCKETFNLYYMESDDDHGVKFREHQFTKIDTIAADESFTQMDLGDRILKLNTEIREVGPVNKKGFYLAFQDVGACVALVSVRVYFKK 201
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196     


Chain B from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l0p B  27 AVADRYAVYWNSSNPRFQRGDYHIDVCINDYLDVFCPHYEDSVPEDKTERYVLYMVNFDGYSACDHTSKGFKRWECNRPHSPNGPLKFSEKFQLFTPFSLGFEFRPGREYFYISSAIPDNGRRSCLKLKVFVRPTNSCM 165
                                    36        46        56        66        76        86        96       106       116       126       136       146       156
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  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 4L0P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L0P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L0P)

(-) Gene Ontology  (58, 66)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ile B:143 - Pro B:144   [ RasMol ]  
    Tyr A:47 - Pro A:48   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        EFNA5_HUMAN | P52803: 2x11 3mx0 4bk5 4bka 4m4r
        EPHA3_HUMAN | P29320: 2gsf 2qo2 2qo7 2qo9 2qob 2qoc 2qod 2qof 2qoi 2qok 2qol 2qon 2qoo 2qoq 3dzq 3fxx 3fy2 4g2f 4gk2 4gk3 4gk4 4p4c 4p5q 4p5z 4twn 4two

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4L0P)