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(-) Description

Title :  CRYSTAL STRUCTURE OF THE EPHA4 LBD IN COMPLEX WITH APYD3 PEPTIDE INHIBITOR
 
Authors :  B. C. Lechtenberg, E. J. Olson, E. B. Pasquale, P. E. Dawson, S. J. Riedl
Date :  05 May 16  (Deposition) - 06 Jul 16  (Release) - 05 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,E  (1x)
Biol. Unit 2:  B,F  (1x)
Biol. Unit 3:  C,G  (1x)
Biol. Unit 4:  D,H  (1x)
Keywords :  Receptor Tyrosine Kinase, Peptide Inhibitor, Ephrin, Als, Transferase-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. J. Olson, B. C. Lechtenberg, C. Zhao, E. Rubio De La Torre, I. Lamberto, S. J. Riedl, P. E. Dawson, E. B. Pasquale
Modifications Of A Nanomolar Cyclic Peptide Antagonist For The Epha4 Receptor To Achieve High Plasma Stability.
Acs Med. Chem. Lett. V. 7 841 2016
PubMed-ID: 27660688  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.6B00132

(-) Compounds

Molecule 1 - EPHRIN TYPE-A RECEPTOR 4
    Chains: A, B, C, D
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: EPHA4, HEK8, SEK, TYRO1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: EPH-LIKE KINASE 8,HEK8,TYROSINE-PROTEIN KINASE TYRO1, TYROSINE-PROTEIN KINASE RECEPTOR SEK
 
Molecule 2 - APYD3 PEPTIDE
    Chains: E, F, G, H
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A   E   
Biological Unit 2 (1x):  B   F  
Biological Unit 3 (1x):   C   G 
Biological Unit 4 (1x):    D   H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 26)

Asymmetric Unit (4, 26)
No.NameCountTypeFull Name
1BAL8Mod. Amino AcidBETA-ALANINE
2GOL8Ligand/IonGLYCEROL
3HEZ6Ligand/IonHEXANE-1,6-DIOL
4NH24Mod. Amino AcidAMINO GROUP
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1BAL2Mod. Amino AcidBETA-ALANINE
2GOL3Ligand/IonGLYCEROL
3HEZ2Ligand/IonHEXANE-1,6-DIOL
4NH21Mod. Amino AcidAMINO GROUP
Biological Unit 2 (4, 9)
No.NameCountTypeFull Name
1BAL2Mod. Amino AcidBETA-ALANINE
2GOL3Ligand/IonGLYCEROL
3HEZ3Ligand/IonHEXANE-1,6-DIOL
4NH21Mod. Amino AcidAMINO GROUP
Biological Unit 3 (4, 5)
No.NameCountTypeFull Name
1BAL2Mod. Amino AcidBETA-ALANINE
2GOL1Ligand/IonGLYCEROL
3HEZ1Ligand/IonHEXANE-1,6-DIOL
4NH21Mod. Amino AcidAMINO GROUP
Biological Unit 4 (3, 4)
No.NameCountTypeFull Name
1BAL2Mod. Amino AcidBETA-ALANINE
2GOL1Ligand/IonGLYCEROL
3HEZ-1Ligand/IonHEXANE-1,6-DIOL
4NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (30, 30)

Asymmetric Unit (30, 30)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:170 , ARG A:171 , LYS A:202 , HOH A:463 , HOH A:472 , HOH A:520binding site for residue HEZ A 301
02AC2SOFTWARESER A:48 , ASN A:81 , TRP A:83 , ARG A:85 , ILE A:137 , GLU A:139 , PHE A:142 , HOH A:439 , HOH A:455 , LEU D:50 , GLU D:51binding site for residue HEZ A 302
03AC3SOFTWAREGLU A:30 , GLU A:100 , ARG A:198binding site for residue GOL A 303
04AC4SOFTWAREARG A:96 , ASP A:172 , VAL A:173 , GLY A:174 , HOH A:434 , HOH A:438 , HOH A:522binding site for residue GOL A 304
05AC5SOFTWAREASP A:158 , GLY A:160binding site for residue GOL A 305
06AC6SOFTWAREILE B:170 , ARG B:171 , LYS B:202 , HOH B:467binding site for residue HEZ B 301
07AC7SOFTWARETHR B:104 , LEU B:105 , PHE B:154 , LYS B:165 , ASN B:167 , HOH B:476binding site for residue HEZ B 302
08AC8SOFTWAREGLY B:93 , ALA B:94 , GLN B:95 , ARG B:96 , TYR B:201 , LYS B:202 , HOH B:402 , HOH B:460 , HOH B:525binding site for residue HEZ B 303
09AC9SOFTWAREPRO B:27 , GLU B:30 , GLU B:100 , ARG B:198binding site for residue GOL B 304
10AD1SOFTWAREASP B:158 , GLY B:160 , HOH B:404binding site for residue GOL B 305
11AD2SOFTWAREARG B:96 , ASP B:172 , VAL B:173 , GLY B:174 , HOH B:457binding site for residue GOL B 306
12AD3SOFTWARESER C:48 , ARG C:85 , ILE C:137 , GLU C:139 , PHE C:142 , HOH C:403 , HOH C:478 , HOH C:499 , HOH C:533binding site for residue HEZ C 301
13AD4SOFTWAREARG C:96 , ASP C:172 , VAL C:173 , GLY C:174 , HOH C:455 , HOH C:490binding site for residue GOL C 302
14AD5SOFTWAREARG D:96 , ASP D:172 , VAL D:173 , GLY D:174 , HOH D:483binding site for residue GOL D 301
15AD6SOFTWARECYS A:73 , ASN A:74 , GLU A:77 , TYR E:3 , CYS E:4binding site for Di-peptide BAL E 1 and PRO E 2
16AD7SOFTWAREARG A:162 , HOH A:452 , VAL E:5 , TYR E:6 , SER E:9 , HOH E:103 , HOH E:105binding site for Di-peptide ARG E 7 and BAL E 8
17AD8SOFTWAREARG A:162 , TYR E:6 , ARG E:7 , TRP E:10 , SER E:11 , HOH E:102binding site for Di-peptide BAL E 8 and SER E 9
18AD9SOFTWARETYR E:3 , CYS E:4 , SER E:11binding site for Di-peptide CYS E 12 and NH2 E 13
19AE1SOFTWARECYS B:73 , ASN B:74 , GLU B:77 , TYR F:3 , CYS F:4 , HOH F:102binding site for Di-peptide BAL F 1 and PRO F 2
20AE2SOFTWAREARG B:162 , HOH B:420 , VAL F:5 , TYR F:6 , SER F:9 , HOH F:106 , HOH F:108binding site for Di-peptide ARG F 7 and BAL F 8
21AE3SOFTWAREARG B:162 , TYR F:6 , ARG F:7 , TRP F:10 , HOH F:104binding site for Di-peptide BAL F 8 and SER F 9
22AE4SOFTWARETYR F:3 , CYS F:4 , SER F:11binding site for Di-peptide CYS F 12 and NH2 F 13
23AE5SOFTWARECYS C:73 , ASN C:74 , GLU C:77 , PRO D:112 , GLY D:113 , HOH D:463 , TYR G:3 , CYS G:4 , HOH G:102binding site for Di-peptide BAL G 1 and PRO G 2
24AE6SOFTWAREILE C:59 , HOH C:480 , VAL G:5 , TYR G:6 , SER G:9 , HOH G:103 , HOH G:105binding site for Di-peptide ARG G 7 and BAL G 8
25AE7SOFTWAREARG C:162 , HOH C:404 , TYR G:6 , ARG G:7 , TRP G:10 , SER G:11 , HOH G:103binding site for Di-peptide BAL G 8 and SER G 9
26AE8SOFTWAREGLY D:113 , MET D:115 , HOH D:468 , TYR G:3 , CYS G:4 , SER G:11 , HOH G:106binding site for Di-peptide CYS G 12 and NH2 G 13
27AE9SOFTWAREGLY D:52 , CYS D:73 , ASN D:74 , GLU D:77 , HOH D:456 , TYR H:3 , CYS H:4 , HOH H:102 , HOH H:104binding site for Di-peptide BAL H 1 and PRO H 2
28AF1SOFTWAREILE D:59 , ARG D:162 , HOH D:431 , VAL H:5 , TYR H:6 , SER H:9 , HOH H:101binding site for Di-peptide ARG H 7 and BAL H 8
29AF2SOFTWARETYR H:6 , ARG H:7 , TRP H:10 , SER H:11 , HOH H:101binding site for Di-peptide BAL H 8 and SER H 9
30AF3SOFTWARETYR H:3 , CYS H:4 , SER H:11 , HOH H:106 , HOH H:107binding site for Di-peptide CYS H 12 and NH2 H 13

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:73 -A:191
2A:108 -A:118
3B:73 -B:191
4B:108 -B:118
5C:73 -C:191
6C:108 -C:118
7D:73 -D:191
8D:108 -D:118
9E:4 -E:12
10F:4 -F:12
11G:4 -G:12
12H:4 -H:12

(-) Cis Peptide Bonds  (11, 14)

Asymmetric Unit
No.Residues
1Ser A:48 -Pro A:49
2Gly A:174 -Pro A:175
3Ser B:48 -Pro B:49
4Gly B:174 -Pro B:175
5Ser C:48 -Pro C:49
6Gly C:174 -Pro C:175
7Ser D:48 -Pro D:49
8Gly D:174 -Pro D:175
9Bal E:1 -Pro E:2
10Bal F:1 -Pro F:2
11Bal G:1 -Pro G:2

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JR2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JR2)

(-) Exons   (0, 0)

(no "Exon" information available for 5JR2)

(-) 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:179
                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh.eeeeee.hhh......eee......eeeeee.....eeeeeeee........eeee...ee......eeeeeeeee.hhhhh.........eeeeeeeee........hhhhheeeeeee....eeeee....eeeeeeeeeee......eeeeeeee...eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jr2 A  26 GPGNEVTLLDSRSVQGELGWIASPLEGGWEEVSIMDEKNTPIRTYQVCNVMEPSQNNWLRTDWITREGAQRVYIEIKFTLRDCNSLPGVMGTCKETFNLYYYESDNDKERFIRENQFVKIDTIAADESFTQVDIGDRIMKLNTEIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKKA 204
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195         


Chain B from PDB  Type:PROTEIN  Length:179
                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh.eeeeee.hhh......eee......eeeeee.....eeeeeeee........eeee...ee......eeeeeeeee.hhhhh.........eeeeeeeee........hhhhheeeeeee....eeeee....eeeeeeeeeee......eeeeeeee...eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jr2 B  26 GPGNEVTLLDSRSVQGELGWIASPLEGGWEEVSIMDEKNTPIRTYQVCNVMEPSQNNWLRTDWITREGAQRVYIEIKFTLRDCNSLPGVMGTCKETFNLYYYESDNDKERFIRENQFVKIDTIAADESFTQVDIGDRIMKLNTEIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKKA 204
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195         


Chain C from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh.eeeeee.hhh......eee......eeeeee...eeeeeee.........eeee...ee......eeeeeeeee.hhhhh.......eeeeeeeee........hhhhheeeeeee....eeeee....eeeeeeeeeee......eeeeeeee....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jr2 C  26 GPGNEVTLLDSRSVQGELGWIASPLEGGWEEVSIMDNTPIRTYQVCNVMEPSQNNWLRTDWITREGAQRVYIEIKFTLRDCNSLPGGTCKETFNLYYYESDNDKERFIRENQFVKIDTIAADESFTQVDIGDRIMKLNTEIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKKA 204
                                    35        45        55     || 67        77        87        97       107     ||119       129       139       149       159       169       179       189       199     
                                                              61|                                              113|                                                                                        
                                                               64                                               116                                                                                        


Chain D from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh.eeeeee.hhh......eee......eeeee....eeeeee.........eeee...ee......eeeeeeeee.hhhhh.........eeeeeeeee........hhhhheeeeeee....eeeee....eeeeeeeeeee......eeeeeeee....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jr2 D  26 GPGNEVTLLDSRSVQGELGWIASPLEGGWEEVSIMNTPIRTYQVCNVMEPSQNNWLRTDWITREGAQRVYIEIKFTLRDCNSLPGVMGTCKETFNLYYYESDNDKERFIRENQFVKIDTIAADESFTQVDIGDRIMKLNTEIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKKA 204
                                    35        45        55    ||  68        78        88        98       108       118       128       138       148       158       168       178       188       198      
                                                             60|                                                                                                                                            
                                                              64                                                                                                                                            


Chain E from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ....ee...ee.. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 5jr2 E   1 xPYCVYRxSWSCx  13
                            |      |10  |
                            1-BAL  8-BAL|
                                       13-NH2


Chain F from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ....ee...ee.. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 5jr2 F   1 xPYCVYRxSWSCx  13
                            |      |10  |
                            |      8-BAL|
                            1-BAL      13-NH2


Chain G from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ....ee...ee.. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 5jr2 G   1 xPYCVYRxSWSCx  13
                            |      |10  |
                            |      8-BAL|
                            1-BAL      13-NH2


Chain H from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ....ee...ee.. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 5jr2 H   1 xPYCVYRxSWSCx  13
                            |      |10  |
                            |      8-BAL|
                            1-BAL      13-NH2
   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 5JR2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JR2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JR2)

(-) Gene Ontology  (66, 66)

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  5jr2
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  EPHA4_HUMAN | P54764
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(-) 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 4m4p 4m4r 4w4z 4w50

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5JR2)