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(-) Description

Title :  CRYSTAL STRUCTURE OF EPHRIN A2 (EPHA2) RECEPTOR PROTEIN KINASE WITH ALISERTIB (MLN8237)
 
Authors :  D. Kudlinzki, V. L. Linhard, S. L. Gande, S. Sreeramulu, K. Saxena, S. He G. Medard, B. Kuester, H. Schwalbe
Date :  21 Feb 16  (Deposition) - 09 Nov 16  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Transferase, Tyrosine-Protein Kinase, Receptor, Atp-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Heinzlmeir, D. Kudlinzki, S. Sreeramulu, S. Klaeger, S. L. Gande, V. Linhard, M. Wilhelm, H. Qiao, D. Helm, B. Ruprecht, K. Saxena, G. Medard, H. Schwalbe, B. Kuster
Chemical Proteomics And Structural Biology Define Epha2 Inhibition By Clinical Kinase Drugs.
Acs Chem. Biol. V. 11 3400 2016
PubMed-ID: 27768280  |  Reference-DOI: 10.1021/ACSCHEMBIO.6B00709

(-) Compounds

Molecule 1 - EPHRIN TYPE-A RECEPTOR 2
    Chains: A, B, C
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 596-900
    Gene: EPHA2, ECK
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: LIGAND ID UNL: UNKNOWN LIGAND ALISERTIB EDO FROM CRYO SOAKING
    Synonym: EPITHELIAL CELL KINASE,TYROSINE-PROTEIN KINASE RECEPTOR ECK

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 23)

Asymmetric Unit (2, 23)
No.NameCountTypeFull Name
1A5B3Ligand/IonALISERTIB
2EDO20Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1A5B1Ligand/IonALISERTIB
2EDO6Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1A5B1Ligand/IonALISERTIB
2EDO9Ligand/Ion1,2-ETHANEDIOL
Biological Unit 3 (2, 6)
No.NameCountTypeFull Name
1A5B1Ligand/IonALISERTIB
2EDO5Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:619 , ALA A:621 , ALA A:644 , LYS A:646 , GLU A:663 , TYR A:694 , MET A:695 , GLU A:696 , GLY A:698 , LYS A:702 , LEU A:746 , SER A:756 , HOH A:1110 , HOH A:1157 , HOH A:1171 , HOH A:1182binding site for residue A5B A 1001
02AC2SOFTWARELYS A:617 , TYR A:694binding site for residue EDO A 1002
03AC3SOFTWAREALA A:731 , LYS A:863 , PHE A:864 , ALA A:865 , HOH A:1106binding site for residue EDO A 1003
04AC4SOFTWAREASN A:750 , HOH A:1258binding site for residue EDO A 1004
05AC5SOFTWAREGLN A:852 , ARG A:860 , PRO A:862 , EDO A:1006 , ASP C:888 , ARG C:890binding site for residue EDO A 1005
06AC6SOFTWAREARG A:861 , LYS A:863 , ASP A:866 , EDO A:1005binding site for residue EDO A 1006
07AC7SOFTWAREHIS A:672 , ALA A:725 , LYS A:728 , HOH A:1178 , HOH A:1210binding site for residue EDO A 1007
08AC8SOFTWAREILE B:619 , ALA B:621 , ALA B:644 , LYS B:646 , GLU B:663 , TYR B:694 , MET B:695 , GLU B:696 , GLY B:698 , LYS B:702 , ASN B:744 , LEU B:746 , SER B:756 , HOH B:1153 , HOH B:1157 , HOH B:1164 , HOH B:1222binding site for residue A5B B 1001
09AC9SOFTWAREARG B:835 , GLN C:616binding site for residue EDO B 1002
10AD1SOFTWAREGLN A:616 , LYS A:617 , ASN B:750 , HOH B:1106 , HOH B:1156 , HOH B:1274binding site for residue EDO B 1003
11AD2SOFTWAREARG B:705 , ASP B:708 , THR B:812 , TYR B:813 , HOH B:1176binding site for residue EDO B 1004
12AD3SOFTWAREGLU B:693 , TYR B:694 , MET B:695 , GLU B:696 , ASN B:748binding site for residue EDO B 1005
13AD4SOFTWAREARG B:705 , GLU B:706 , HOH B:1115 , HOH B:1125binding site for residue EDO B 1006
14AD5SOFTWAREPHE B:670 , ARG B:677 , LEU B:678 , HOH B:1136 , HOH B:1141binding site for residue EDO B 1007
15AD6SOFTWARELYS B:617 , ILE B:619binding site for residue EDO B 1008
16AD7SOFTWAREVAL B:601 , LEU B:602 , LYS B:603 , PHE B:604binding site for residue EDO B 1009
17AD8SOFTWAREALA B:731 , LYS B:863 , PHE B:864 , ALA B:865 , HOH B:1172binding site for residue EDO B 1010
18AD9SOFTWAREILE C:619 , ALA C:621 , ALA C:644 , LYS C:646 , TYR C:694 , MET C:695 , GLU C:696 , GLY C:698 , LYS C:702 , ARG C:743 , ASN C:744 , LEU C:746 , SER C:756 , EDO C:1003 , HOH C:1101 , HOH C:1120 , HOH C:1134 , HOH C:1194binding site for residue A5B C 1001
19AE1SOFTWAREPHE C:604 , THR C:605 , THR C:606 , GLY C:668 , LEU C:678 , GLU C:679 , GLY C:680binding site for residue EDO C 1002
20AE2SOFTWARELYS C:617 , ILE C:619 , TYR C:694 , A5B C:1001 , HOH C:1121 , HOH C:1134binding site for residue EDO C 1003
21AE3SOFTWAREARG C:738binding site for residue EDO C 1004
22AE4SOFTWAREALA C:731 , LYS C:863 , PHE C:864 , ALA C:865 , HOH C:1165binding site for residue EDO C 1005
23AE5SOFTWAREASP A:888 , GLN C:852 , ARG C:860binding site for residue EDO C 1006

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IA0)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Lys A:686 -Pro A:687
2Lys B:686 -Pro B:687
3Lys C:686 -Pro C:687

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IA0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IA0)

(-) Exons   (0, 0)

(no "Exon" information available for 5IA0)

(-) 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:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhh.eeeeeeeee....eeeeeee....eeeeeee.....hhhhhhhhhhhhhhhhh........eeeee......eeeee....eehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ia0 A 604 FTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTKEVPVAIKTLKAGYTEKQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFGIPIRWTAPEAISYRKFTSASDVWSFGIVMWEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARRPKFADIVSILDKLIRAPDSLKTLADFDP 889
                                   613       623       633||     647       657       667       677       687       697       707       717       727       737       747       757 ||    786       796       806       816       826       836       846       856       866       876       886   
                                                        634|                                                                                                                     759|                                                                                                              
                                                         639                                                                                                                      779                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.hhh.eeeeeeeee....eeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhh.........eeeee.....eeeeee.....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ia0 B 600 AVLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTSKEVPVAIKTLKAGYTEKQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFGLSRVLIPIRWTAPEAISYRKFTSASDVWSFGIVMWEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARRPKFADIVSILDKLIRAPDSLK 882
                                   609       619       629     ||642       652       662       672       682       692       702       712       722       732       742       752       762 ||    786       796       806       816       826       836       846       856       866       876      
                                                             635|                                                                                                                          764|                                                                                                       
                                                              639                                                                                                                           779                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:269
                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhh.eeeeeeeee....eeeeeeee....eeeeeeee....hhhhhhhhhhhhhhh.........eeeee......eeeee.....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ia0 C 600 AVLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTGKKEVPVAIKTLKATEKQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFGLSPIRWTAPEAISYRKFTSASDVWSFGIVMWEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARRPKFADIVSILDKLIRAPDSLKTLADFDPR 890
                                   609       619       629    || 641       653       663       673       683       693       703       713       723       733       743       753       781       791       801       811       821       831       841       851       861       871       881         
                                                            634|          650|                                                                                                         761|                                                                                                              
                                                             637           653                                                                                                          780
   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 5IA0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IA0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IA0)

(-) Gene Ontology  (62, 62)

Asymmetric Unit(hide GO term definitions)

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  EPHA2_HUMAN | P29317
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 Related Entries

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

UniProtKB/Swiss-Prot
        EPHA2_HUMAN | P29317: 1mqb 2e8n 2k9y 2kso 2x10 2x11 3c8x 3czu 3fl7 3hei 3hpn 3kka 3mbw 3mx0 3skj 4p2k 4pdo 4trl 5ek7 5i9u 5i9v 5i9w 5i9x 5i9y 5i9z 5ia1 5ia2 5ia3 5ia4 5ia5 5njz 5nk0 5nk1 5nk2 5nk3 5nk4 5nk5 5nk6 5nk7 5nk8 5nk9 5nka 5nkb 5nkc 5nkd 5nke 5nkf 5nkg 5nkh 5nki

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