4W50 - JenaLib

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Title :   STRUCTURE OF THE EPHA4 LBD IN COMPLEX WITH PEPTIDE

Authors :   B. C. Lechtenberg, P. D. Mace, S. J. Riedl

Date :   16 Aug 14 (Deposition) - 08 Oct 14 (Release) - 14 Jan 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.42

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, Transferase-Transferase Inhibitor Complex (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

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	:	LIGAND BINDING DOMAIN, 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 PEPTIDE
	Chains	:	E, F, G, H
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
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)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	BU2	4	Ligand/Ion	1,3-BUTANEDIOL
2	GOL	6	Ligand/Ion	GLYCEROL

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	BU2	1	Ligand/Ion	1,3-BUTANEDIOL
2	GOL	3	Ligand/Ion	GLYCEROL

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	BU2	1	Ligand/Ion	1,3-BUTANEDIOL
2	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	BU2	1	Ligand/Ion	1,3-BUTANEDIOL
2	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 4 (2, 2)

No.	Name	Count	Type	Full Name
1	BU2	1	Ligand/Ion	1,3-BUTANEDIOL
2	GOL	1	Ligand/Ion	GLYCEROL

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:30 , ILE A:170 , LYS A:202 , ILE D:170 , ARG D:171 , ASP D:172	binding site for residue BU2 A 301
02	AC2	SOFTWARE	ARG A:85 , PHE A:136 , ILE A:137 , HOH A:439	binding site for residue GOL A 302
03	AC3	SOFTWARE	GLU A:62 , ASP A:158 , GLY A:160	binding site for residue GOL A 303
04	AC4	SOFTWARE	ARG A:96 , GLY A:174 , GLY B:160	binding site for residue GOL A 304
05	AC5	SOFTWARE	ILE B:170 , ASP B:172 , ILE C:170 , LYS C:202	binding site for residue BU2 B 301
06	AC6	SOFTWARE	ARG B:85 , ARG B:135 , PHE B:136 , ILE B:137	binding site for residue GOL B 302
07	AC7	SOFTWARE	GLU B:30 , ARG B:198 , ASP C:151 , SER C:153 , GLU C:169	binding site for residue BU2 C 301
08	AC8	SOFTWARE	ILE C:46 , SER C:48 , ILE C:137 , GLU C:139 , PHE C:142	binding site for residue GOL C 302
09	AC9	SOFTWARE	ASP A:151 , SER A:153 , GLU D:30 , GLU D:100 , ARG D:198	binding site for residue BU2 D 301
10	AD1	SOFTWARE	TRP D:83 , PHE D:136 , ILE D:137 , GLU D:139	binding site for residue GOL D 302

Asymmetric Unit

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

Asymmetric Unit

No.	Residues
1	Ser A:48	-	Pro A:49
2	Gly A:174	-	Pro A:175
3	Ser B:48	-	Pro B:49
4	Gly B:174	-	Pro B:175
5	Ser C:48	-	Pro C:49
6	Gly C:174	-	Pro C:175
7	Ser D:48	-	Pro D:49
8	Gly D:174	-	Pro D:175

(no "SAP(SNP)/Variant" information available for 4W50)

(no "PROSITE Motif" information available for 4W50)

(no "Exon" information available for 4W50)

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.hhh......eee......eeeeee.....eeeeeee.........eeee...ee......eeeeeeeee...............eeeeeeeee........hhhhheeeeeee....eeeee....eeeeeeeeeee......eeeeeeee....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w50 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......eeeeeeeeeehhhhh.........eeeeeeeee.............eeeeeee....eeeee....eeeeeeeeeee......eeeeeeee...eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w50 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:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhh......eee......eeeee.......eeeeee.........eeee...ee......eeeeeeeee...............eeeeeeeee........hhhhheeeeeee...eeeeee....eeeeeeeeeee......eeeeeeee....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w50 C  28 GNEVTLLDSRSVQGELGWIASPLEGGWEEVSIMDEKNTPIRTYQVCNVMEPSQNNWLRTDWITREGAQRVYIEIKFTLRDCNSLPGVMGTCKETFNLYYYESDNDKERFIRENQFVKIDTIAADESFTQVDIGDRIMKLNTEIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKKA 204
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197

Chain D from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhh......eee......eeeee.......eeeeee.........eeee...ee......eeeeeeeee.hhhhh.........eeeeeeeee........hhhhheeeeeee...eeeeee....eeeeeeeeeee......eeeeeeee....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w50 D  28 GNEVTLLDSRSVQGELGWIASPLEGGWEEVSIMDEKNTPIRTYQVCNVMEPSQNNWLRTDWITREGAQRVYIEIKFTLRDCNSLPGVMGTCKETFNLYYYESDNDKERFIRENQFVKIDTIAADESFTQVDIGDRIMKLNTEIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKKA 204
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197

Chain E from PDB  Type:PROTEIN  Length:12
                                            
               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
                 4w50 E   1 APYCVYRGSWSC  12
                                    10

Chain F from PDB  Type:PROTEIN  Length:12
                                            
               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
                 4w50 F   1 APYCVYRGSWSC  12
                                    10

Chain G from PDB  Type:PROTEIN  Length:12
                                            
               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
                 4w50 G   1 APYCVYRGSWSC  12
                                    10

Chain H from PDB  Type:PROTEIN  Length:12
                                            
               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
                 4w50 H   1 APYCVYRGSWSC  12
                                    10

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 '\|'

(no "SCOP Domain" information available for 4W50)

(no "CATH Domain" information available for 4W50)

(no "Pfam Domain" information available for 4W50)

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	Cis Peptide Bonds
		Gly A:174 - Pro A:175	[ RasMol ]
		Gly B:174 - Pro B:175	[ RasMol ]
		Gly C:174 - Pro C:175	[ RasMol ]
		Gly D:174 - Pro D:175	[ RasMol ]
		Ser A:48 - Pro A:49	[ RasMol ]
		Ser B:48 - Pro B:49	[ RasMol ]
		Ser C:48 - Pro C:49	[ RasMol ]
		Ser D:48 - Pro D:49	[ RasMol ]

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	4w50
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	2.7.10.1
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	EPHA4_HUMAN \| P54764	:	2lw8 2wo1 2wo2 2wo3 3ckh 3gxu 4bk4 4bk5 4bka 4bkf 4m4p 4m4r 4w4z 5jr2

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (10, 10)

SS Bonds (12, 12)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (66, 66)

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