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(-) Description

Title :  STRUCTURE OF THE EPHA4 LBD IN COMPLEX WITH PEPTIDE
 
Authors :  B. C. Lechtenberg, P. D. Mace, S. J. Riedl
Date :  15 Aug 14  (Deposition) - 08 Oct 14  (Release) - 07 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.41
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 :  Protein-Inhibitor Complex, Ligand Binding Domain, Signal Transduction, Receptor-Tyrosine Kinase, Cyclic Peptide, Epha4, Phage Display (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Lamberto, B. C. Lechtenberg, E. J. Olson, P. D. Mace, P. E. Dawson, S. J. Riedl, E. B. Pasquale
Development And Structural Analysis Of A Nanomolar Cyclic Peptide Antagonist For The Epha4 Receptor.
Acs Chem. Biol. V. 9 2787 2014
PubMed-ID: 25268696  |  Reference-DOI: 10.1021/CB500677X

(-) 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 Plasmid: NKI HIS-3C-LIC
    Expression System Strain: ORIGAMI 2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 29-204
    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 - APY-BALA8.AM 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, 29)

Asymmetric Unit (4, 29)
No.NameCountTypeFull Name
1BAL4Mod. Amino AcidBETA-ALANINE
2GOL14Ligand/IonGLYCEROL
3HEZ7Ligand/IonHEXANE-1,6-DIOL
4NH24Mod. Amino AcidAMINO GROUP
Biological Unit 1 (4, 7)
No.NameCountTypeFull Name
1BAL1Mod. Amino AcidBETA-ALANINE
2GOL3Ligand/IonGLYCEROL
3HEZ2Ligand/IonHEXANE-1,6-DIOL
4NH21Mod. Amino AcidAMINO GROUP
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
1BAL1Mod. Amino AcidBETA-ALANINE
2GOL4Ligand/IonGLYCEROL
3HEZ2Ligand/IonHEXANE-1,6-DIOL
4NH21Mod. Amino AcidAMINO GROUP
Biological Unit 3 (3, 6)
No.NameCountTypeFull Name
1BAL1Mod. Amino AcidBETA-ALANINE
2GOL4Ligand/IonGLYCEROL
3HEZ-1Ligand/IonHEXANE-1,6-DIOL
4NH21Mod. Amino AcidAMINO GROUP
Biological Unit 4 (4, 8)
No.NameCountTypeFull Name
1BAL1Mod. Amino AcidBETA-ALANINE
2GOL3Ligand/IonGLYCEROL
3HEZ3Ligand/IonHEXANE-1,6-DIOL
4NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (33, 33)

Asymmetric Unit (33, 33)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:48 , ASN A:81 , TRP A:83 , ILE A:137 , GLU A:139binding site for residue HEZ A 301
02AC2SOFTWARESER A:153 , THR A:168 , GLU A:169 , ILE A:170 , SER D:153 , THR D:168 , HOH D:434binding site for residue HEZ A 302
03AC3SOFTWAREGLU A:30 , GLU A:100 , ARG A:198 , ASP D:151binding site for residue GOL A 303
04AC4SOFTWAREARG A:96 , GLY A:174 , ASP B:161 , GLN D:95 , TYR D:98 , HEZ D:303binding site for residue GOL A 304
05AC5SOFTWARELEU A:34 , ASP A:35 , SER A:38 , GLY D:28binding site for residue GOL A 305
06AC6SOFTWARETYR B:98 , ILE B:170 , ARG B:171 , LYS B:202 , HOH B:422 , ILE C:170 , ASP C:172 , LYS C:202binding site for residue HEZ B 301
07AC7SOFTWARESER B:153 , THR B:168 , GLU B:169 , ILE B:170 , SER C:153 , THR C:168 , GLU C:169 , ILE C:170binding site for residue HEZ B 302
08AC8SOFTWAREGLY B:52 , GLY B:53 , GLU B:55 , GLN B:71 , VAL B:72 , CYS B:73 , ASN B:74 , PRO F:2 , HOH F:102binding site for residue GOL B 303
09AC9SOFTWARETRP B:83 , ARG B:85 , PHE B:136 , ILE B:137 , HOH B:438binding site for residue GOL B 304
10AD1SOFTWAREARG B:96 , VAL B:173 , GLY B:174binding site for residue GOL B 305
11AD2SOFTWARETHR B:32 , LEU B:34 , ASP B:35binding site for residue GOL B 306
12AD3SOFTWAREILE A:59 , MET A:60 , ILE A:159 , ARG A:162 , GLN C:95 , PRO C:175 , LEU C:176 , SER C:177 , ARG E:7binding site for residue GOL C 301
13AD4SOFTWARETYR B:98 , LYS B:202 , ARG C:96 , ASP C:172 , GLY C:174binding site for residue GOL C 302
14AD5SOFTWAREGLY B:28 , LEU C:33 , LEU C:34 , ASP C:35 , SER C:38binding site for residue GOL C 303
15AD6SOFTWARESER C:48 , TRP C:83 , ILE C:137 , GLU C:139binding site for residue GOL C 304
16AD7SOFTWAREILE A:170 , LYS A:202 , ILE D:170 , ARG D:171 , ASP D:172 , LYS D:202 , HOH D:422binding site for residue HEZ D 301
17AD8SOFTWARESER D:48 , ASN D:81 , PHE D:136 , ILE D:137 , GLU D:139 , PHE D:142binding site for residue HEZ D 302
18AD9SOFTWAREGOL A:304 , GLY D:93 , ALA D:94 , GLN D:95 , ARG D:96 , TYR D:98 , TYR D:201 , LYS D:202binding site for residue HEZ D 303
19AE1SOFTWAREARG D:96 , ASP D:172 , VAL D:173 , GLY D:174binding site for residue GOL D 304
20AE2SOFTWAREGLY A:28 , LYS A:203 , THR D:32 , LEU D:33 , ASP D:35 , SER D:38 , VAL D:39binding site for residue GOL D 305
21AE3SOFTWAREPRO H:2 , TYR H:3 , SER H:11 , CYS H:12 , NH2 H:13binding site for residue GOL H 101
22AE4SOFTWAREILE A:59 , GLU C:128 , PRO C:175 , SER C:177 , GOL C:301 , VAL E:5 , TYR E:6 , SER E:9 , HOH E:102binding site for Di-peptide ARG E 7 and BAL E 8
23AE5SOFTWAREARG A:162 , TYR E:6 , ARG E:7 , TRP E:10 , SER E:11 , HOH E:102 , HOH E:103binding site for Di-peptide BAL E 8 and SER E 9
24AE6SOFTWARETYR E:3 , CYS E:4 , SER E:11binding site for Di-peptide CYS E 12 and NH2 E 13
25AE7SOFTWAREARG B:162 , PRO D:175 , TYR F:6 , SER F:9binding site for Di-peptide ARG F 7 and BAL F 8
26AE8SOFTWAREARG B:162 , TYR F:6 , ARG F:7 , TRP F:10 , SER F:11binding site for Di-peptide BAL F 8 and SER F 9
27AE9SOFTWARETYR F:3 , CYS F:4 , SER F:11binding site for Di-peptide CYS F 12 and NH2 F 13
28AF1SOFTWAREILE C:59 , VAL G:5 , TYR G:6 , SER G:9 , HOH G:101binding site for Di-peptide ARG G 7 and BAL G 8
29AF2SOFTWAREARG C:162 , TYR G:6 , ARG G:7 , TRP G:10 , SER G:11binding site for Di-peptide BAL G 8 and SER G 9
30AF3SOFTWARETYR G:3 , CYS G:4 , SER G:11binding site for Di-peptide CYS G 12 and NH2 G 13
31AF4SOFTWAREILE D:59 , VAL H:5 , TYR H:6 , SER H:9binding site for Di-peptide ARG H 7 and BAL H 8
32AF5SOFTWAREARG D:162 , VAL H:5 , TYR H:6 , ARG H:7 , TRP H:10binding site for Di-peptide BAL H 8 and SER H 9
33AF6SOFTWARETYR H:3 , CYS H:4 , SER H:11 , GOL H:101binding 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  (8, 8)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4W4Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W4Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4W4Z)

(-) 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:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..........eee......eeeeee.....eeeeeee.........eeee...ee......eeeeeeeee.hhhhh.........eeeeeeeee........hhhhheeeeeee....eeeee....eeeeeeeeeee......eeeeeeee....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w4z A  28 GNEVTLLDSRSVQGELGWIASPLEGGWEEVSIMDEKNTPIRTYQVCNVMEPSQNNWLRTDWITREGAQRVYIEIKFTLRDCNSLPGVMGTCKETFNLYYYESDNDKERFIRENQFVKIDTIAADESFTQVDIGDRIMKLNTEIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKKA 204
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       


Chain B from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhh......eee......eeeeee.....eeeeeee.........eeee...ee......eeeeeeeeee..............eeeeeeeee........hhhhheeeeeee....eeeee....eeeeeeeeeee......eeeeeeee...eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w4z B  28 GNEVTLLDSRSVQGELGWIASPLEGGWEEVSIMDEKNTPIRTYQVCNVMEPSQNNWLRTDWITREGAQRVYIEIKFTLRDCNSLPGVMGTCKETFNLYYYESDNDKERFIRENQFVKIDTIAADESFTQVDIGDRIMKLNTEIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKKA 204
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       


Chain C from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhh......eee......eeeeee...eeeeeee.........eeee...ee......eeeeeeeee...............eeeeeeeee........hhhhheeeeeee...eeeeee....eeeeeeeeeee......eeeeeeee....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w4z C  28 GNEVTLLDSRSVQGELGWIASPLEGGWEEVSIMDNTPIRTYQVCNVMEPSQNNWLRTDWITREGAQRVYIEIKFTLRDCNSLPGVMGTCKETFNLYYYESDNDKERFIRENQFVKIDTIAADESFTQVDIGDRIMKLNTEIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKKA 204
                                    37        47        57   ||   69        79        89        99       109       119       129       139       149       159       169       179       189       199     
                                                            61|                                                                                                                                            
                                                             64                                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.hhh......eee......eeeee....eeeeeee........eeee...ee......eeeeeeeee.hhhhh.........eeeeeeeee.............eeeeeee....eeeee....eeeeeeeeeee......eeeeeeee...eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4w4z D  28 GNEVTLLDSRSVQGELGWIASPLEGGWEEVSIMDTPIRTYQVCNVMEPSQNNWLRTDWITREGAQRVYIEIKFTLRDCNSLPGVMGTCKETFNLYYYESDNDKERFIRENQFVKIDTIAADESFTQVDIGDRIMKLNTEIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKKA 204
                                    37        47        57   ||   70        80        90       100       110       120       130       140       150       160       170       180       190       200    
                                                            61|                                                                                                                                           
                                                             65                                                                                                                                           


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
                 4w4z E   1 APYCVYRxSWSCx  13
                                   |10  |
                                   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
                 4w4z F   1 APYCVYRxSWSCx  13
                                   |10  |
                                   8-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
                 4w4z G   1 APYCVYRxSWSCx  13
                                   |10  |
                                   8-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
                 4w4z H   1 APYCVYRxSWSCx  13
                                   |10  |
                                   8-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 4W4Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4W4Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W4Z)

(-) Gene Ontology  (66, 66)

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  4w4z
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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 4m4p 4m4r 4w50 5jr2

(-) Related Entries Specified in the PDB File

4w50