1R1P - JenaLib

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Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Biological Unit 7 (Jmol Viewer)

Title :   STRUCTURAL BASIS FOR DIFFERENTIAL RECOGNITION OF TYROSINE PHOSPHORYLATED SITES IN THE LINKER FOR ACTIVATION OF T CELLS (LAT) BY THE ADAPTOR PROTEIN GADS

Authors :   S. Cho, R. A. Mariuzza

Date :   24 Sep 03 (Deposition) - 28 Sep 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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)
Biol. Unit 5: A,B,C,D,E,F,G,H  (1x)
Biol. Unit 6: A,B,E,F  (1x)
Biol. Unit 7: C,D,G,H  (1x)

Keywords :   Sh2, Gads, Phosphopeptide, Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Cho, C. A. Velikovsky, C. P. Swaminathan, J. C. Houtman, L. E. Samelson, R. A. Mariuzza
Structural Basis For Differential Recognition Of Tyrosine-Phosphorylated Sites In The Linker For Activation Of T Cells (Lat) By The Adaptor Gads.
Embo J. V. 23 1441 2004
PubMed-ID: 15029250 | Reference-DOI: 10.1038/SJ.EMBOJ.7600168
(for further references see the PDB file header)

Molecule 1 - GRB2-RELATED ADAPTOR PROTEIN 2
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	GADS-SH2 DOMAIN
	Gene	:	GADS
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	GADS PROTEIN, GROWTH FACTOR RECEPTOR BINDING PROTEIN, GRBLG, GRB-2-LIKE PROTEIN, GRB2L, HEMATOPOIETIC CELL-ASSOCIATED ADAPTOR PROTEIN GRPL, GRB-2-RELATED MONOCYTIC ADAPTER PROTEIN, MONOCYTIC ADAPTER, MONA, ADAPTER PROTEIN GRID

Molecule 2 - LAT PY171 PEPTIDE
	Chains	:	E, F, G, H
	Engineered	:	YES
	Other Details	:	THE PEPTIDE WAS CHEMICALLY SYNTHESIZED
	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
Biological Unit 5 (1x)	:	A	B	C	D	E	F	G	H
Biological Unit 6 (1x)	:	A	B			E	F
Biological Unit 7 (1x)	:			C	D			G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 18)

No.	Name	Count	Type	Full Name
1	ACE	4	Mod. Amino Acid	ACETYL GROUP
2	PTR	4	Mod. Amino Acid	O-PHOSPHOTYROSINE
3	SO4	10	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 4)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 4 (3, 5)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 5 (3, 18)

No.	Name	Count	Type	Full Name
1	ACE	4	Mod. Amino Acid	ACETYL GROUP
2	PTR	4	Mod. Amino Acid	O-PHOSPHOTYROSINE
3	SO4	10	Ligand/Ion	SULFATE ION

Biological Unit 6 (3, 9)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	PTR	2	Mod. Amino Acid	O-PHOSPHOTYROSINE
3	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 7 (3, 9)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	PTR	2	Mod. Amino Acid	O-PHOSPHOTYROSINE
3	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TRP A:120 , THR A:121 , GLU A:122 , TYR A:133 , TYR A:134 , LYS A:141	BINDING SITE FOR RESIDUE SO4 A 500
02	AC2	SOFTWARE	ARG A:148 , TRP B:120 , THR B:121 , GLU B:122 , TYR B:133 , TYR B:134 , LYS B:141 , HOH B:511 , HOH B:554 , HOH B:572	BINDING SITE FOR RESIDUE SO4 B 501
03	AC3	SOFTWARE	TRP C:120 , THR C:121 , GLU C:122 , TYR C:133 , TYR C:134 , LYS C:141 , HOH C:539	BINDING SITE FOR RESIDUE SO4 C 502
04	AC4	SOFTWARE	ARG C:148 , TRP D:120 , THR D:121 , GLU D:122 , TYR D:133 , TYR D:134 , LYS D:141 , HOH D:515	BINDING SITE FOR RESIDUE SO4 D 503
05	AC5	SOFTWARE	ASP A:112 , THR A:113 , LYS A:114 , ASP B:112 , THR B:113	BINDING SITE FOR RESIDUE SO4 B 504
06	AC6	SOFTWARE	ASP C:112 , THR C:113 , ASP D:112 , THR D:113	BINDING SITE FOR RESIDUE SO4 D 505
07	AC7	SOFTWARE	SER D:126 , ASN D:128 , LYS D:129	BINDING SITE FOR RESIDUE SO4 D 506
08	AC8	SOFTWARE	SER C:126 , ASN C:128 , LYS C:129 , HOH C:598	BINDING SITE FOR RESIDUE SO4 C 507
09	AC9	SOFTWARE	SER A:126 , ASN A:128 , LYS A:129 , HOH A:577	BINDING SITE FOR RESIDUE SO4 A 508
10	BC1	SOFTWARE	SER B:126 , ASN B:128 , LYS B:129 , HOH B:549 , HOH B:558 , HOH B:585	BINDING SITE FOR RESIDUE SO4 B 509

(no "SS Bond" information available for 1R1P)

(no "Cis Peptide Bond" information available for 1R1P)

(no "SAP(SNP)/Variant" information available for 1R1P)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH2	PS50001	Src homology 2 (SH2) domain profile.	GRAP2_MOUSE	58-149	4	A:60-149 B:60-149 C:60-149 D:60-149

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.	GRAP2_MOUSE	58-149	1	A:60-149 - - -

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.	GRAP2_MOUSE	58-149	1	- B:60-149 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH2	PS50001	Src homology 2 (SH2) domain profile.	GRAP2_MOUSE	58-149	1	- - C:60-149 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH2	PS50001	Src homology 2 (SH2) domain profile.	GRAP2_MOUSE	58-149	1	- - - D:60-149

Biological Unit 5 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH2	PS50001	Src homology 2 (SH2) domain profile.	GRAP2_MOUSE	58-149	4	A:60-149 B:60-149 C:60-149 D:60-149

Biological Unit 6 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH2	PS50001	Src homology 2 (SH2) domain profile.	GRAP2_MOUSE	58-149	2	A:60-149 B:60-149 - -

Biological Unit 7 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH2	PS50001	Src homology 2 (SH2) domain profile.	GRAP2_MOUSE	58-149	2	- - C:60-149 D:60-149

(no "Exon" information available for 1R1P)

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:95
 aligned with GRAP2_MOUSE | O89100 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:95
                                    62        72        82        92       102       112       122       132       142     
          GRAP2_MOUSE    53 IEFPEWFHEGLSRHQAENLLMGKDIGFFIIRASQSSPGDFSISVRHEDDVQHFKVMRDTKGNYFLWTEKFPSLNKLVDYYRTTSISKQKQVFLRD 147
               SCOP domains d1r1pa_ A: GRB2-related adaptor protein 2 (MONA, GRID)                                          SCOP domains
               CATH domains 1r1pA00 A:55-149 SHC Adaptor Protein                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhh.....eeeee.......eeeeee....eeeee.ee.....ee....ee.hhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SH2  PDB: A:60-149 UniProt: 58-149                                                         PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 1r1p A  55 IEFPEWFHEGLSRHQAENLLMGKDIGFFIIRASQSSPGDFSISVRHEDDVQHFKVMRDTKGNYFLWTEKFPSLNKLVDYYRTTSISKQKQVFLRD 149
                                    64        74        84        94       104       114       124       134       144

Chain B from PDB  Type:PROTEIN  Length:100
 aligned with GRAP2_MOUSE | O89100 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:108
                                    49        59        69        79        89        99       109       119       129       139        
          GRAP2_MOUSE    40 GSQEGYVPKNFIDIEFPEWFHEGLSRHQAENLLMGKDIGFFIIRASQSSPGDFSISVRHEDDVQHFKVMRDTKGNYFLWTEKFPSLNKLVDYYRTTSISKQKQVFLRD 147
               SCOP domains d1        r1pb_ B: GRB2-related adaptor protein 2 (MONA, GRID)                                               SCOP domains
               CATH domains 1r        1pB00 B:50-149 SHC Adaptor Protein                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..--------..............hhhhhhhhhhh.....eeeee.......eeeeee....eeeee.ee.....ee....ee.hhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------SH2  PDB: B:60-149 UniProt: 58-149                                                         PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1r1p B  50 GS--------FIDIEFPEWFHEGLSRHQAENLLMGKDIGFFIIRASQSSPGDFSISVRHEDDVQHFKVMRDTKGNYFLWTEKFPSLNKLVDYYRTTSISKQKQVFLRD 149
                             |       -|       61        71        81        91       101       111       121       131       141        
                            51       52

Chain C from PDB  Type:PROTEIN  Length:100
 aligned with GRAP2_MOUSE | O89100 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:108
                                    49        59        69        79        89        99       109       119       129       139        
          GRAP2_MOUSE    40 GSQEGYVPKNFIDIEFPEWFHEGLSRHQAENLLMGKDIGFFIIRASQSSPGDFSISVRHEDDVQHFKVMRDTKGNYFLWTEKFPSLNKLVDYYRTTSISKQKQVFLRD 147
               SCOP domains d1        r1pc_ C: GRB2-related adaptor protein 2 (MONA, GRID)                                               SCOP domains
               CATH domains 1r        1pC00 C:50-149 SHC Adaptor Protein                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..--------..............hhhhhhhhhhh.....eeeee.......eeeeee....eeeee.ee.....ee.......hhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------SH2  PDB: C:60-149 UniProt: 58-149                                                         PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1r1p C  50 GS--------FIDIEFPEWFHEGLSRHQAENLLMGKDIGFFIIRASQSSPGDFSISVRHEDDVQHFKVMRDTKGNYFLWTEKFPSLNKLVDYYRTTSISKQKQVFLRD 149
                             |       -|       61        71        81        91       101       111       121       131       141        
                            51       52

Chain D from PDB  Type:PROTEIN  Length:95
 aligned with GRAP2_MOUSE | O89100 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:95
                                    62        72        82        92       102       112       122       132       142     
          GRAP2_MOUSE    53 IEFPEWFHEGLSRHQAENLLMGKDIGFFIIRASQSSPGDFSISVRHEDDVQHFKVMRDTKGNYFLWTEKFPSLNKLVDYYRTTSISKQKQVFLRD 147
               SCOP domains d1r1pd_ D: GRB2-related adaptor protein 2 (MONA, GRID)                                          SCOP domains
               CATH domains 1r1pD00 D:55-149 SHC Adaptor Protein                                                            CATH domains
           Pfam domains (1) -----SH2-1r1pD01 D:60-134                                                       --------------- Pfam domains (1)
           Pfam domains (2) -----SH2-1r1pD02 D:60-134                                                       --------------- Pfam domains (2)
           Pfam domains (3) -----SH2-1r1pD03 D:60-134                                                       --------------- Pfam domains (3)
           Pfam domains (4) -----SH2-1r1pD04 D:60-134                                                       --------------- Pfam domains (4)
         Sec.struct. author ...........hhhhhhhhhhh.....eeeee.......eeeeee....eeeee.ee.....ee....ee.hhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SH2  PDB: D:60-149 UniProt: 58-149                                                         PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 1r1p D  55 IEFPEWFHEGLSRHQAENLLMGKDIGFFIIRASQSSPGDFSISVRHEDDVQHFKVMRDTKGNYFLWTEKFPSLNKLVDYYRTTSISKQKQVFLRD 149
                                    64        74        84        94       104       114       124       134       144

Chain E from PDB  Type:PROTEIN  Length:7
                                       
               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
                 1r1p E 555 xDDyVNV 561
                            |  |   
                          555-ACE  
                             558-PTR

Chain F from PDB  Type:PROTEIN  Length:7
                                       
               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
                 1r1p F 555 xDDyVNV 561
                            |  |   
                            |  |   
                          555-ACE  
                             558-PTR

Chain G from PDB  Type:PROTEIN  Length:7
                                       
               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
                 1r1p G 555 xDDyVNV 561
                            |  |   
                            |  |   
                          555-ACE  
                             558-PTR

Chain H from PDB  Type:PROTEIN  Length:7
                                       
               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
                 1r1p H 555 xDDyVNV 561
                            |  |   
                            |  |   
                          555-ACE  
                             558-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(

)

Folds(

)

Superfamilies( (-)

)

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: GRB2-related adaptor protein 2 (MONA, GRID) (3)

Mouse (Mus musculus) [TaxId: 10090] (3)

1a	d1r1pa_	A:
1b	d1r1pb_	B:
1c	d1r1pc_	C:
1d	d1r1pd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: SHC Adaptor Protein (206)

Homologous Superfamily: SHC Adaptor Protein (206)

House mouse (Mus musculus) (17)

1a	1r1pB00	B:50-149
1b	1r1pD00	D:55-149
1c	1r1pC00	C:50-149
1d	1r1pA00	A:55-149

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: SH2 (119)

Mus musculus (Mouse) (12)

1a	SH2-1r1pD01	D:60-134
1b	SH2-1r1pD02	D:60-134
1c	SH2-1r1pD03	D:60-134
1d	SH2-1r1pD04	D:60-134

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (GRAP2_MOUSE | O89100)

molecular function
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1r1p)

Biological Units
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	1r1p
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	GRAP2_MOUSE \| O89100	:	1h3h 1oeb 1r1q 1r1s 1uti 2d0n 2w10

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 18)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (1, 4)

Gene Ontology (5, 5)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File