2V76 - JenaLib

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)

Title :   CRYSTAL STRUCTURE OF THE HUMAN DOK1 PTB DOMAIN

Authors :   C. L. Oxley, N. J. Anthis, E. D. Lowe, I. D. Campbell, K. L. Wegener

Date :   26 Jul 07 (Deposition) - 08 Jan 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Alternative Splicing, Protein-Binding, Ptb Domain, Phosphorylation, Adaptor Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. L. Oxley, N. J. Anthis, E. D. Lowe, I. Vakonakis, I. D. Campbell, K. L. Wegener
An Integrin Phosphorylation Switch: The Effect Of {Beta}3 Integrin Tail Phosphorylation On Dok1 And Talin Binding.
J. Biol. Chem. V. 283 5420 2008
PubMed-ID: 18156175 | Reference-DOI: 10.1074/JBC.M709435200

Molecule 1 - DOCKING PROTEIN 1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Fragment	:	PTB DOMAIN, RESIDUES 152-256
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DOWNSTREAM OF TYROSINE KINASE 1, P62, DOK, PP62, HUMAN DOK1 PTB

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	1	Ligand/Ion	GLYCEROL
3	PGE	4	Ligand/Ion	TRIETHYLENE GLYCOL
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	-1	Ligand/Ion	GLYCEROL
3	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	-1	Ligand/Ion	GLYCEROL
3	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	1	Ligand/Ion	GLYCEROL
3	PGE	-1	Ligand/Ion	TRIETHYLENE GLYCOL
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 4 (2, 2)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	-1	Ligand/Ion	GLYCEROL
3	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL
4	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN B:6 , TRP B:8 , ARG C:19 , PRO C:77	BINDING SITE FOR RESIDUE PGE B1107
02	AC2	SOFTWARE	ARG A:19 , GLN D:6 , TRP D:8 , HOH D:2005 , HOH D:2083 , HOH D:2084 , HOH D:2085 , HOH D:2086	BINDING SITE FOR RESIDUE PGE D1104
03	AC3	SOFTWARE	ARG B:19 , PRO B:77 , HOH B:2030 , HOH B:2102 , HOH B:2103 , HOH B:2104 , GLN C:6 , TRP C:8 , VAL C:27	BINDING SITE FOR RESIDUE PGE B1108
04	AC4	SOFTWARE	GLN A:6 , TRP A:8 , ARG D:19 , PRO D:77	BINDING SITE FOR RESIDUE PGE A1105
05	AC5	SOFTWARE	ARG D:59 , GLY D:73 , ARG D:74 , ARG D:75	BINDING SITE FOR RESIDUE SO4 D1105
06	AC6	SOFTWARE	ARG B:59 , GLY B:73 , ARG B:74 , HOH B:2105 , HOH B:2106	BINDING SITE FOR RESIDUE SO4 B1109
07	AC7	SOFTWARE	ARG A:59 , GLY A:73 , ARG A:74 , HOH A:2097	BINDING SITE FOR RESIDUE SO4 A1106
08	AC8	SOFTWARE	HOH B:2028 , GLN C:89 , ASP C:92 , HIS C:102 , HOH C:2092 , HOH C:2093 , HOH C:2094	BINDING SITE FOR RESIDUE SO4 C1107
09	AC9	SOFTWARE	ARG C:60 , TYR C:61 , GLU C:98 , HOH C:2095	BINDING SITE FOR RESIDUE GOL C1108
10	BC1	SOFTWARE	ARG A:60 , TYR A:61 , GLU A:98 , HOH A:2099	BINDING SITE FOR RESIDUE EDO A1107

(no "SS Bond" information available for 2V76)

(no "Cis Peptide Bond" information available for 2V76)

(no "SAP(SNP)/Variant" information available for 2V76)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IRS_PTB	PS51064	IRS-type PTB domain profile.	DOK1_HUMAN	151-259	1	A:4-104

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IRS_PTB	PS51064	IRS-type PTB domain profile.	DOK1_HUMAN	151-259	1	A:4-104

Biological Unit 2 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IRS_PTB	PS51064	IRS-type PTB domain profile.	DOK1_HUMAN	151-259	0	-

Biological Unit 3 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IRS_PTB	PS51064	IRS-type PTB domain profile.	DOK1_HUMAN	151-259	0	-

Biological Unit 4 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IRS_PTB	PS51064	IRS-type PTB domain profile.	DOK1_HUMAN	151-259	0	-

Asymmetric Unit (3, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3a	ENST00000233668	3a	ENSE00001254734	chr2:74781213-74781941	729	DOK1_HUMAN	1-20	20	0	-	-
1.4d	ENST00000233668	4d	ENSE00001732324	chr2:74782281-74782580	300	DOK1_HUMAN	21-120	100	0	-	-
1.4j	ENST00000233668	4j	ENSE00001701285	chr2:74782702-74782795	94	DOK1_HUMAN	121-152	32	1	A:2-4 (gaps) - - -	5 - - -
1.5b	ENST00000233668	5b	ENSE00001742360	chr2:74783021-74783205	185	DOK1_HUMAN	152-213	62	4	A:4-65 (gaps) B:5-65 C:5-65 D:5-65	62 61 61 61
1.6h	ENST00000233668	6h	ENSE00001872726	chr2:74783435-74784681	1247	DOK1_HUMAN	214-481	268	4	A:66-104 B:66-106 C:66-106 D:66-103	39 41 41 38

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:99
 aligned with DOK1_HUMAN | Q99704 from UniProtKB/Swiss-Prot  Length:481

    Alignment length:105
                                   157       167       177       187       197       207       217       227       237       247     
           DOK1_HUMAN   148 PTWEGSQFWVTVQRTEAAERCGLHGSYVLRVEAERLTLLTVGAQSQILEPLLSWPYTLLRRYGRDKVMFSFEAGRRCPSGPGTFTFQTAQGNDIFQAVETAIHRQ 252
               SCOP domains d  2v76a_ A: automated matches                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--..eeeeeee..hhhhhhh....eeeeee...eeeeeee.----.eeeeeeee...eeeeee...eeeeee........eeeeee..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---IRS_PTB  PDB: A:4-104 UniProt: 151-259                                                                 PROSITE
           Transcript 1 (1) 1.4j -------------------------------------------------------------Exon 1.6h  PDB: A:66-104 [INCOMPLETE]   Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.5b  PDB: A:4-65 (gaps) UniProt: 152-213                --------------------------------------- Transcript 1 (2)
                 2v76 A   2 P--LGSQFWVTVQRTEAAERCGLHGSYVLRVEAERLTLLTVG----ILEPLLSWPYTLLRRYGRDKVMFSFEAGRRCPSGPGTFTFQTAQGNDIFQAVETAIHRQ 104
                            |  |     9        19        29        39 |    | 49        59        69        79        89        99     
                            |  3                                    41   46                                                          
                            2

Chain B from PDB  Type:PROTEIN  Length:102
 aligned with DOK1_HUMAN | Q99704 from UniProtKB/Swiss-Prot  Length:481

    Alignment length:102
                                   162       172       182       192       202       212       222       232       242       252  
           DOK1_HUMAN   153 SQFWVTVQRTEAAERCGLHGSYVLRVEAERLTLLTVGAQSQILEPLLSWPYTLLRRYGRDKVMFSFEAGRRCPSGPGTFTFQTAQGNDIFQAVETAIHRQKA 254
               SCOP domains d2v76b_ B: automated matches                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..hhhhhhh....eeeeee...eeeeeee......eeeeeeee...eeeeee...eeeeee........eeeeee..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE IRS_PTB  PDB: - UniProt: 151-259                                                                       PROSITE
           Transcript 1 (1) -------------------------------------------------------------Exon 1.6h  PDB: B:66-106 UniProt: 214-481 Transcript 1 (1)
           Transcript 1 (2) Exon 1.5b  PDB: B:5-65 UniProt: 152-213 [INCOMPLETE]         ----------------------------------------- Transcript 1 (2)
                 2v76 B   5 SQFWVTVQRTEAAERCGLHGSYVLRVEAERLTLLTVGAQSQILEPLLSWPYTLLRRYGRDKVMFSFEAGRRCPSGPGTFTFQTAQGNDIFQAVETAIHRQKA 106
                                    14        24        34        44        54        64        74        84        94       104

Chain C from PDB  Type:PROTEIN  Length:102
 aligned with DOK1_HUMAN | Q99704 from UniProtKB/Swiss-Prot  Length:481

    Alignment length:102
                                   162       172       182       192       202       212       222       232       242       252  
           DOK1_HUMAN   153 SQFWVTVQRTEAAERCGLHGSYVLRVEAERLTLLTVGAQSQILEPLLSWPYTLLRRYGRDKVMFSFEAGRRCPSGPGTFTFQTAQGNDIFQAVETAIHRQKA 254
               SCOP domains d2v76c_ C: automated matches                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..hhhhhhh....eeeeee...eeeeeee......eeeeeeee...eeeeee...eeeeee........eeeeee..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE IRS_PTB  PDB: - UniProt: 151-259                                                                       PROSITE
           Transcript 1 (1) -------------------------------------------------------------Exon 1.6h  PDB: C:66-106 UniProt: 214-481 Transcript 1 (1)
           Transcript 1 (2) Exon 1.5b  PDB: C:5-65 UniProt: 152-213 [INCOMPLETE]         ----------------------------------------- Transcript 1 (2)
                 2v76 C   5 SQFWVTVQRTEAAERCGLHGSYVLRVEAERLTLLTVGAQSQILEPLLSWPYTLLRRYGRDKVMFSFEAGRRCPSGPGTFTFQTAQGNDIFQAVETAIHRQKA 106
                                    14        24        34        44        54        64        74        84        94       104

Chain D from PDB  Type:PROTEIN  Length:99
 aligned with DOK1_HUMAN | Q99704 from UniProtKB/Swiss-Prot  Length:481

    Alignment length:99
                                   162       172       182       192       202       212       222       232       242         
           DOK1_HUMAN   153 SQFWVTVQRTEAAERCGLHGSYVLRVEAERLTLLTVGAQSQILEPLLSWPYTLLRRYGRDKVMFSFEAGRRCPSGPGTFTFQTAQGNDIFQAVETAIHR 251
               SCOP domains d2v76d_ D: automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) IRS-2v76D01 D:5-103                                                                                 Pfam domains (1)
           Pfam domains (2) IRS-2v76D02 D:5-103                                                                                 Pfam domains (2)
           Pfam domains (3) IRS-2v76D03 D:5-103                                                                                 Pfam domains (3)
           Pfam domains (4) IRS-2v76D04 D:5-103                                                                                 Pfam domains (4)
         Sec.struct. author .eeeeee..hhhhhhh....eeeeee...eeeeeee......eeeeeeee...eeeeee...eeeeee........eeeeee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE IRS_PTB  PDB: - UniProt: 151-259                                                                    PROSITE
           Transcript 1 (1) -------------------------------------------------------------Exon 1.6h  PDB: D:66-103 [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) Exon 1.5b  PDB: D:5-65 UniProt: 152-213 [INCOMPLETE]         -------------------------------------- Transcript 1 (2)
                 2v76 D   5 SQFWVTVQRTEAAERCGLHGSYVLRVEAERLTLLTVGAQSQILEPLLSWPYTLLRRYGRDKVMFSFEAGRRCPSGPGTFTFQTAQGNDIFQAVETAIHR 103
                                    14        24        34        44        54        64        74        84        94

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Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: PH domain-like barrel (258)

Superfamily: PH domain-like (257)

Family: Phosphotyrosine-binding domain (PTB) (31)

Protein domain: automated matches (6)

Human (Homo sapiens) [TaxId: 9606] (3)

1a	d2v76a_	A:
1b	d2v76b_	B:
1c	d2v76c_	C:
1d	d2v76d_	D:

(no "CATH Domain" information available for 2V76)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: IRS] (14)

Family: IRS (14)

Homo sapiens (Human) (5)

1a	IRS-2v76D01	D:5-103
1b	IRS-2v76D02	D:5-103
1c	IRS-2v76D03	D:5-103
1d	IRS-2v76D04	D:5-103

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DOK1_HUMAN | Q99704)

molecular function
	GO:0005158	insulin receptor binding	Interacting selectively and non-covalently with the insulin receptor.
	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).
	GO:0005057	signal transducer activity, downstream of receptor	Conveys a signal from an upstream receptor or intracellular signal transducer, converting the signal into a form where it can ultimately trigger a change in the state or activity of a cell.
biological process
	GO:0007265	Ras protein signal transduction	A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
	GO:0007166	cell surface receptor signaling pathway	A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	GO:0045742	positive regulation of epidermal growth factor receptor signaling pathway	Any process that activates or increases the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

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	2v76
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Description

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Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)

SS Bonds (0, 0)

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Exons (3, 9)

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