1XOD - JenaLib

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Title :   CRYSTAL STRUCTURE OF X. TROPICALIS SPRED1 EVH-1 DOMAIN

Authors :   N. J. Harmer, J. M. Sivak, E. Amaya, T. L. Blundell

Date :   06 Oct 04 (Deposition) - 25 Jan 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.15

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Spred, Sprouty, Evh1, Peptide-Binding, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. J. Harmer, J. M. Sivak, E. Amaya, T. L. Blundell
1. 15A Crystal Structure Of The X. Tropicalis Spred1 Evh1 Domain Suggests A Fourth Distinct Peptide-Binding Mechanism Within The Evh1 Family
Febs Lett. V. 579 1161 2005
PubMed-ID: 15710406 | Reference-DOI: 10.1016/J.FEBSLET.2004.11.114

Molecule 1 - SPRED1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETG-10A
	Expression System Strain	:	ER2566
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	EVH-1 DOMAIN
	Gene	:	SPRED1
	Organism Common	:	WESTERN CLAWED FROG
	Organism Scientific	:	XENOPUS TROPICALIS
	Organism Taxid	:	8364

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS B:81 , VAL B:82 , THR B:83 , PRO B:84 , HOH B:453 , HOH B:458 , HOH B:492 , HOH B:493	BINDING SITE FOR RESIDUE GOL B 401

(no "SS Bond" information available for 1XOD)

(no "Cis Peptide Bond" information available for 1XOD)

(no "SAP(SNP)/Variant" information available for 1XOD)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	WH1	PS50229	WH1 domain profile.	SPRE1_XENTR	3-120	1	B:6-120

Biological Unit 1 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	WH1	PS50229	WH1 domain profile.	SPRE1_XENTR	3-120	0	-

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	WH1	PS50229	WH1 domain profile.	SPRE1_XENTR	3-120	1	B:6-120

(no "Exon" information available for 1XOD)

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
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Chain A from PDB  Type:PROTEIN  Length:106
 aligned with SPRE1_XENTR | Q66JG9 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:114
                                    19        29        39        49        59        69        79        89        99       109       119    
          SPRE1_XENTR    10 SYARVRAVVMTRDDSSGGWLQLGGGGLSSVTVSKTLQPGDSGGTEFLVHGERLRDKTVVLECVLRRDLVYNKVTPTFHHWRIGDKKFGLTFQSPADARAFDRGIRRAIEDLSQG 123
               SCOP domains d1xoda1 A:10-123 Sprouty-related, E        VH1 domain-containing protein 1, Spred-1                                SCOP domains
               CATH domains 1xodA00 A:10-123 Pleckstrin-homolog        y domain (PH domain)/Phosphotyrosine-binding domain (PTB)               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeee......eee.hhh..eeeeee..--------...eeeeee.....eeeeee.....eeeeee..eeeeee..eeeeeee.hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE WH1  PDB: - UniProt: 3-120                                                                                     --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1xod A  10 SYARVRAVVMTRDDSSGGWLQLGGGGLSSVTVSKT--------TEFLVHGERLRDKTVVLECVLRRDLVYNKVTPTFHHWRIGDKKFGLTFQSPADARAFDRGIRRAIEDLSQG 123
                                    19        29        39    |    -   |    59        69        79        89        99       109       119    
                                                             44       53

Chain B from PDB  Type:PROTEIN  Length:118
 aligned with SPRE1_XENTR | Q66JG9 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:121
                                    12        22        32        42        52        62        72        82        92       102       112       122 
          SPRE1_XENTR     3 GEQEPDDSYARVRAVVMTRDDSSGGWLQLGGGGLSSVTVSKTLQPGDSGGTEFLVHGERLRDKTVVLECVLRRDLVYNKVTPTFHHWRIGDKKFGLTFQSPADARAFDRGIRRAIEDLSQG 123
               SCOP domains d   1xodb_ B: automated matches                                                                                           SCOP domains
               CATH domains 1   xodB00 B:6-123 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)                            CATH domains
           Pfam domains (1) ------WH1-1xodB01 B:9-117                                                                                          ------ Pfam domains (1)
           Pfam domains (2) ------WH1-1xodB02 B:9-117                                                                                          ------ Pfam domains (2)
         Sec.struct. author .---...eeeeeeeeeeee......eee.hhh..eeeeeee...........eeeeeee....eeeeeeee......eeee..eeeeee..eeeeeee.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE WH1  PDB: B:6-120 UniProt: 3-120                                                                                      --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xod B   6 G---SDDSYARVRAVVMTRDDSSGGWLQLGGGGLSSVTVSKTLQPGDSGGTEFLVHGERLRDKTVVLECVLRRDLVYNKVTPTFHHWRIGDKKFGLTFQSPADARAFDRGIRRAIEDLSQG 123
                            |   |   12        22        32        42        52        62        72        82        92       102       112       122 
                            6   7

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: PH-domain like (150)

Homologous Superfamily: Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) (147)

Western clawed frog (Xenopus tropicalis) (2)

1a	1xodB00	B:6-123
1b	1xodA00	A:10-123

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PH (111)

Family: WH1 (6)

Xenopus tropicalis (Western clawed frog) (Silurana tropicalis) (2)

1a	WH1-1xodB01	B:9-117
1b	WH1-1xodB02	B:9-117

Asymmetric Unit(hide GO term definitions)

Chain A,B (SPRE1_XENTR | Q66JG9)

molecular function
	GO:0019902	phosphatase binding	Interacting selectively and non-covalently with any phosphatase.
biological process
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0010923	negative regulation of phosphatase activity	Any process that decreases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0009966	regulation of signal transduction	Any process that modulates the frequency, rate or extent of signal transduction.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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	SPRE1_XENTR \| Q66JG9	:	1tj6

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Description

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Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

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