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(-) Description

Title :  CRYSTAL STRUCTURE OF EPHA4 ECTODOMAIN
 
Authors :  K. Xu, D. Tsvetkova-Robev, Y. Xu, Y. Goldgur, Y. -P. Chan, J. P. Himanen, D. B. Nikolov
Date :  07 Aug 13  (Deposition) - 30 Oct 13  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym./Biol. Unit :  A
Keywords :  Eph Receptor Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Xu, D. Tzvetkova-Robev, Y. Xu, Y. Goldgur, Y. P. Chan, J. P. Himanen, D. B. Nikolov
Insights Into Eph Receptor Tyrosine Kinase Activation From Crystal Structures Of The Epha4 Ectodomain And Its Complex With Ephrin-A5.
Proc. Natl. Acad. Sci. Usa V. 110 14634 2013
PubMed-ID: 23959867  |  Reference-DOI: 10.1073/PNAS.1311000110

(-) Compounds

Molecule 1 - EPHRIN TYPE-A RECEPTOR 4
    Chains: A
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Organ: OVARY
    Expression System Strain: HIGH5
    Expression System Taxid: 7111
    Expression System Vector: PACGP67
    Fragment: UNP RESIDUES 27-543
    Gene: EPHA4, HEK8, SEK, TYRO1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: EPH-LIKE KINASE 8, EK8, HEK8, TYROSINE-PROTEIN KINASE TYRO1, TYROSINE-PROTEIN KINASE RECEPTOR SEK

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:235 , ASN A:236BINDING SITE FOR MONO-SACCHARIDE NAG A 601 BOUND TO ASN A 235
2AC2SOFTWAREASN A:340BINDING SITE FOR MONO-SACCHARIDE NAG A 602 BOUND TO ASN A 340
3AC3SOFTWAREHIS A:406 , ASN A:408BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 408 RESIDUES 603 TO 604

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:73 -A:191
2A:108 -A:118
3A:204 -A:247
4A:233 -A:260
5A:262 -A:273
6A:276 -A:290
7A:293 -A:307
8A:309 -A:325
9A:366 -A:380
10A:369 -A:377

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Leu A:43 -Gly A:44
2Ser A:48 -Pro A:49
3Lys A:63 -Asn A:64
4Gly A:174 -Pro A:175
5Asn A:235 -Asn A:236
6Gly A:355 -Gly A:356
7His A:385 -Tyr A:386
8Thr A:387 -Pro A:388

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M4P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M4P)

(-) Exons   (0, 0)

(no "Exon" information available for 4M4P)

(-) 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:513
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..........eee......eeeeee.....eeeeeee.........eeee...ee......eeeeeeeee.hhhhh.........eeeeeeeee.............eeeeeee.hhhhheee....eeeeeeeeeee......eeeeeeee....eeeeeeeeeeeee..eee..eee..ee.......eeeee.ee...eeeeeeeeeeee........eeeeee...eeee..eeee....ee.........ee....ee.........ee.......................eeeeeeee..eeeeeee...........eeeeeeee.............eee.........eeeee......eeeeeeeee........hhh.eeeeeee...........eeeeee....eeeee...........eeeeeeee........eeeee...eeee.......eeeeeeeeee..ee......eeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m4p A  27 PANEVTLLDSRSVQGELGWIASPLEGGWEEVSIMDEKNTPIRTYQVCNVMEPSQNNWLRTDWITREGAQRVYIEIKFTLRDCNSLPGVMGTCKETFNLYYYESDNDKERFIRENQFVKIDTIAADESFTQVDIGDRIMKLNTEIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKKCPLTVRNLAQFPDTITGADTSSLVEVRGSCVNNSEEKDVPKMYCGADGEWLVPIGNCLCNAGHEERSGECQACKIGYYKALSTDATCAKCPPHSYSVWEGATSCTCDRGFFRADNDAASMPCTRPPSAPLNLISNVNETSVNLEWSSPQNTGGRQDISYNVVCKKCGPSKCRPCGSGVHYTPQQNGLKTTKVSITDLLAHTNYTFEIWAVNGVSKYNPNPDQSVSVTVTTNQAAPSSIALVQAKEVTRYSVALAWLEPDRPNGVILEYEVKYYEKDQNERSYRIVRTAARNTDIKGLNPLTSYVFHVRARTAAGYGDFSEPLEVTTNTVPSRIIGD 542
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366   ||  379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539   
                                                                                                                                                                                                                                                                                                                                                                                 370|                                                                                                                                                                        
                                                                                                                                                                                                                                                                                                                                                                                  374
   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 4M4P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M4P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M4P)

(-) Gene Ontology  (66, 66)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:235 - Asn A:236   [ RasMol ]  
    Gly A:174 - Pro A:175   [ RasMol ]  
    Gly A:355 - Gly A:356   [ RasMol ]  
    His A:385 - Tyr A:386   [ RasMol ]  
    Leu A:43 - Gly A:44   [ RasMol ]  
    Lys A:63 - Asn A:64   [ RasMol ]  
    Ser A:48 - Pro A:49   [ RasMol ]  
    Thr A:387 - Pro A:388   [ RasMol ]  
 

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  4m4p
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  EPHA4_HUMAN | P54764
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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
        EPHA4_HUMAN | P54764: 2lw8 2wo1 2wo2 2wo3 3ckh 3gxu 4bk4 4bk5 4bka 4bkf 4m4r 4w4z 4w50 5jr2

(-) Related Entries Specified in the PDB File

4m4r