1NZV - JenaLib

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Title :   CRYSTAL STRUCTURE OF SRC SH2 DOMAIN BOUND TO DOUBLY PHOSPHORYLATED PEPTIDE PQPYIPYVPA

Authors :   O. Y. Lubman, G. Waksman

Date :   19 Feb 03 (Deposition) - 22 Apr 03 (Release) - 30 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Sh2 Domain, Phosphotyrosine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Y. Lubman, G. Waksman
Structural And Thermodynamic Basis For The Interaction Of The Src Sh2 Domain With The Activated Form Of The Pdgf Beta-Receptor
J. Mol. Biol. V. 328 655 2003
PubMed-ID: 12706723 | Reference-DOI: 10.1016/S0022-2836(03)00344-9

Molecule 1 - TYROSINE-PROTEIN KINASE TRANSFORMING PROTEIN SRC
	Chains	:	A, B
	EC Number	:	2.7.1.112
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET3
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	SH2 DOMAIN
	Gene	:	V-SRC
	Organism Scientific	:	ROUS SARCOMA VIRUS (STRAIN SCHMIDT-RUPPIN)
	Organism Taxid	:	11889
	Strain	:	SCHMIDT-RUPPIN
	Synonym	:	P60-SRC

Molecule 2 - DOUBLY PHOSPHORYLATED PEPTIDE PQPYIPYVPA
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
3	PTR	2	Mod. Amino Acid	O-PHOSPHOTYROSINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
3	PTR	-1	Mod. Amino Acid	O-PHOSPHOTYROSINE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	PG4	-1	Ligand/Ion	TETRAETHYLENE GLYCOL
3	PTR	2	Mod. Amino Acid	O-PHOSPHOTYROSINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:179 , GLU A:180 , THR A:181 , CL A:2001	BINDING SITE FOR RESIDUE CL A 2000
2	AC2	SOFTWARE	HOH A:1092 , CL A:2000	BINDING SITE FOR RESIDUE CL A 2001
3	AC3	SOFTWARE	PHE A:152 , GLU B:252 , HOH B:1108 , HOH B:1109	BINDING SITE FOR RESIDUE PG4 A 3000

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH2	PS50001	Src homology 2 (SH2) domain profile.	SRC_RSVSA	148-245	2	A:150-247 B:254-351

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH2	PS50001	Src homology 2 (SH2) domain profile.	SRC_RSVSA	148-245	1	A:150-247 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH2	PS50001	Src homology 2 (SH2) domain profile.	SRC_RSVSA	148-245	1	- B:254-351

(no "Exon" information available for 1NZV)

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:101
 aligned with SRC_RSVSA | P00524 from UniProtKB/Swiss-Prot  Length:526

    Alignment length:103
                                   154       164       174       184       194       204       214       224       234       244   
            SRC_RSVSA   145 AEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPT 247
               SCOP domains d1nzva_ A: c-src tyrosine kinase                                                                        SCOP domains
               CATH domains 1nzvA00 A:147-249 SHC Adaptor Prote  in                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhh.......eeeeee...--..eeeeeeeee...eeeeeeeeeeee...eee........hhhhhhhhhh...........ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SH2  PDB: A:150-247 UniProt: 148-245                                                              -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1nzv A 147 AEEWYFGKITRRESERLLLNPENPRGTFLVRESET--GAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPT 249
                                   156       166       176    |  186       196       206       216       226       236       246   
                                                            181  |                                                                 
                                                               184

Chain B from PDB  Type:PROTEIN  Length:103
 aligned with SRC_RSVSA | P00524 from UniProtKB/Swiss-Prot  Length:526

    Alignment length:103
                                   154       164       174       184       194       204       214       224       234       244   
            SRC_RSVSA   145 AEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPT 247
               SCOP domains d1nzvb_ B: c-src tyrosine kinase                                                                        SCOP domains
               CATH domains 1nzvB00 B:251-353 SHC Adaptor Protein                                                                   CATH domains
           Pfam domains (1) ---SH2-1nzvB01 B:254-336                                                              ----------------- Pfam domains (1)
           Pfam domains (2) ---SH2-1nzvB02 B:254-336                                                              ----------------- Pfam domains (2)
         Sec.struct. author .........hhhhhhhhhh.......eeeeee.......eeeeeeeee...eeeeeeeeeee.....eeee..eee.hhhhhhhhhhhh.........ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SH2  PDB: B:254-351 UniProt: 148-245                                                              -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1nzv B 251 AEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPT 353
                                   260       270       280       290       300       310       320       330       340       350

Chain C from PDB  Type:PROTEIN  Length:8
                                        
               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
                 1nzv C 498 PQyIyVPA 505
                              | |   
                            500-PTR 
                              502-PTR

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(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: SH2-like (260)

Superfamily: SH2 domain (260)

Family: SH2 domain (225)

Protein domain: c-src tyrosine kinase (62)

Rous sarcoma virus [TaxId: 11886] (12)

1a	d1nzva_	A:
1b	d1nzvb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: SHC Adaptor Protein (206)

Homologous Superfamily: SHC Adaptor Protein (206)

Rous sarcoma virus (strain schmidt- ruppin). Organism_taxid: 11889. Strain: schmidt-ruppin. (2)

1a	1nzvA00	A:147-249
1b	1nzvB00	B:251-353

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: SH2] (119)

Family: SH2 (119)

Avian leukosis virus RSA (RSV-SRA) (Rous sarcoma virus (strain Schmidt-Ruppin A)) (8)

1a	SH2-1nzvB01	B:254-336
1b	SH2-1nzvB02	B:254-336

Asymmetric Unit(hide GO term definitions)

Chain A,B (SRC_RSVSA | P00524)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0004715	non-membrane spanning protein tyrosine kinase activity	Catalysis of the reaction: ATP + protein L-tyrosine = ADP + protein L-tyrosine phosphate by a non-membrane spanning protein.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0004672	protein kinase activity	Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
	GO:0004713	protein tyrosine kinase activity	Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0018108	peptidyl-tyrosine phosphorylation	The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.

Asymmetric Unit
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Biological Units
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	SRC_RSVSA \| P00524	:	1bkl 1bkm 1is0 1kc2 1nzl 1sha 1shb 1skj 1spr 1sps

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