3PS4 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   PDZ DOMAIN FROM HUMAN MICROTUBULE-ASSOCIATED SERINE/THREONINE-PROTEIN KINASE 1

Authors :   E. Ugochukwu, J. Wang, T. Krojer, J. R. C. Muniz, R. Sethi, A. C. W. Pike, A E. Salah, R. Cocking, P. Savitsky, D. A. Doyle, F. Von Delft, C. Bountr C. H. Arrowsmith, J. Weigelt, A. Edwards, S. Knapp, J. M. Elkins, Struc Genomics Consortium (Sgc)

Date :   30 Nov 10 (Deposition) - 29 Dec 10 (Release) - 29 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Structural Genomics, Structural Genomics Consortium, Sgc, Kinase, Pdz Domain, Serine/Threonine-Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Ugochukwu, J. Wang, T. Krojer, J. R. C. Muniz, R. Sethi, A. C. W. Pike, A. Roos, E. Salah, R. Cocking, P. Savitsky, D. A. Doyle, F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, S. Knapp, J. M. Elkins, Structural Genomics Consortium (Sgc)
Pdz Domain From Human Microtubule-Associated Serine/Threonine-Protein Kinase 1
To Be Published
PubMed: search

Molecule 1 - MICROTUBULE-ASSOCIATED SERINE/THREONINE-PROTEIN KINASE 1
	Chains	:	A, B, C, D
	EC Number	:	2.7.11.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)-R3-PRARE2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 965-1057
	Gene	:	MAST1, KIAA0973
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SYNTROPHIN-ASSOCIATED SERINE/THREONINE-PROTEIN KINASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	IMD	3	Ligand/Ion	IMIDAZOLE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	IMD	2	Ligand/Ion	IMIDAZOLE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
2	IMD	1	Ligand/Ion	IMIDAZOLE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:237 , THR A:1051 , THR A:1052 , PRO A:1053	BINDING SITE FOR RESIDUE EDO A 1
2	AC2	SOFTWARE	HIS A:1002 , VAL A:1003 , GLU A:1004 , GLU A:1005 , LYS C:976	BINDING SITE FOR RESIDUE EDO A 1062
3	AC3	SOFTWARE	HOH B:147 , TRP B:1001 , TRP C:1001	BINDING SITE FOR RESIDUE IMD C 1
4	AC4	SOFTWARE	TRP A:1001 , GLU C:1004 , GLU C:1005 , TRP D:1001	BINDING SITE FOR RESIDUE IMD D 1
5	AC5	SOFTWARE	GLY D:1013 , ASP D:1018 , THR D:1051 , THR D:1052 , PHE D:1054	BINDING SITE FOR RESIDUE IMD D 1062

(no "SS Bond" information available for 3PS4)

(no "Cis Peptide Bond" information available for 3PS4)

Asymmetric Unit (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051644	A	1048	S	MAST1_HUMAN	Polymorphism	35052801	A/B/C/D	A	1048	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051644	A	1048	S	MAST1_HUMAN	Polymorphism	35052801	A/D	A	1048	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051644	A	1048	S	MAST1_HUMAN	Polymorphism	35052801	B/C	A	1048	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	MAST1_HUMAN	967-1055	4	A:967-1055 B:967-1055 C:967-1055 D:967-1055

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	MAST1_HUMAN	967-1055	2	A:967-1055 - - D:967-1055

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	MAST1_HUMAN	967-1055	2	- B:967-1055 C:967-1055 -

(no "Exon" information available for 3PS4)

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:96
 aligned with MAST1_HUMAN | Q9Y2H9 from UniProtKB/Swiss-Prot  Length:1570

    Alignment length:96
                                   975       985       995      1005      1015      1025      1035      1045      1055      
         MAST1_HUMAN    966 SPITIQRSGKKYGFTLRAIRVYMGDTDVYSVHHIVWHVEEGGPAQEAGLCAGDLITHVNGEPVHGMVHPEVVELILKSGNKVAVTTTPFENTSIRI 1061
               SCOP domains d3ps4a_ A: automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee.......eeeeeeeee......eeeeeeeeee...hhhhhhh.....eeeee..ee....hhhhhhhhhhhh..eeeeeee.....eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------S------------- SAPs(SNPs)
                    PROSITE -PDZ  PDB: A:967-1055 UniProt: 967-1055                                                   ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                3ps4 A  966 SPITIQRSGKKYGFTLRAIRVYMGDTDVYSVHHIVWHVEEGGPAQEAGLCAGDLITHVNGEPVHGMVHPEVVELILKSGNKVAVTTTPFENTQSLV 1061
                                   975       985       995      1005      1015      1025      1035      1045      1055

Chain B from PDB  Type:PROTEIN  Length:97
 aligned with MAST1_HUMAN | Q9Y2H9 from UniProtKB/Swiss-Prot  Length:1570

    Alignment length:97
                                   974       984       994      1004      1014      1024      1034      1044      1054       
         MAST1_HUMAN    965 RSPITIQRSGKKYGFTLRAIRVYMGDTDVYSVHHIVWHVEEGGPAQEAGLCAGDLITHVNGEPVHGMVHPEVVELILKSGNKVAVTTTPFENTSIRI 1061
               SCOP domains d3ps4b_ B: automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.......eeeeeeeee......eeeeeeeeee...hhhhhhh.....eeeee..ee....hhhhhhhhhhhh..eeeeeee.....eeee Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------S------------- SAPs(SNPs)
                    PROSITE --PDZ  PDB: B:967-1055 UniProt: 967-1055                                                   ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                3ps4 B  965 RSPITIQRSGKKYGFTLRAIRVYMGDTDVYSVHHIVWHVEEGGPAQEAGLCAGDLITHVNGEPVHGMVHPEVVELILKSGNKVAVTTTPFENTQSLV 1061
                                   974       984       994      1004      1014      1024      1034      1044      1054

Chain C from PDB  Type:PROTEIN  Length:96
 aligned with MAST1_HUMAN | Q9Y2H9 from UniProtKB/Swiss-Prot  Length:1570

    Alignment length:96
                                   975       985       995      1005      1015      1025      1035      1045      1055      
         MAST1_HUMAN    966 SPITIQRSGKKYGFTLRAIRVYMGDTDVYSVHHIVWHVEEGGPAQEAGLCAGDLITHVNGEPVHGMVHPEVVELILKSGNKVAVTTTPFENTSIRI 1061
               SCOP domains d3ps4c_ C: automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee.......eeeeeeeee......eeeeeeeeee...hhhhhhh.....eeeee..ee....hhhhhhhhhhhh..eeeeeee.....eeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------S------------- SAPs(SNPs)
                    PROSITE -PDZ  PDB: C:967-1055 UniProt: 967-1055                                                   ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                3ps4 C  966 SPITIQRSGKKYGFTLRAIRVYMGDTDVYSVHHIVWHVEEGGPAQEAGLCAGDLITHVNGEPVHGMVHPEVVELILKSGNKVAVTTTPFENTQSLV 1061
                                   975       985       995      1005      1015      1025      1035      1045      1055

Chain D from PDB  Type:PROTEIN  Length:99
 aligned with MAST1_HUMAN | Q9Y2H9 from UniProtKB/Swiss-Prot  Length:1570

    Alignment length:99
                                   972       982       992      1002      1012      1022      1032      1042      1052         
         MAST1_HUMAN    963 GLRSPITIQRSGKKYGFTLRAIRVYMGDTDVYSVHHIVWHVEEGGPAQEAGLCAGDLITHVNGEPVHGMVHPEVVELILKSGNKVAVTTTPFENTSIRI 1061
               SCOP domains d3ps4d_ D: automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----PDZ-3ps4D01 D:968-1052                                                               --------- Pfam domains (1)
           Pfam domains (2) -----PDZ-3ps4D02 D:968-1052                                                               --------- Pfam domains (2)
           Pfam domains (3) -----PDZ-3ps4D03 D:968-1052                                                               --------- Pfam domains (3)
           Pfam domains (4) -----PDZ-3ps4D04 D:968-1052                                                               --------- Pfam domains (4)
         Sec.struct. author .....eeee.......eeeeeeeee......eeeeeeeeee...hhhhhhh.....eeeee..ee....hhhhhhhhhhhh..eeeeee.......eee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------S------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: D:967-1055 UniProt: 967-1055                                                   ------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                3ps4 D   -1 SMRSPITIQRSGKKYGFTLRAIRVYMGDTDVYSVHHIVWHVEEGGPAQEAGLCAGDLITHVNGEPVHGMVHPEVVELILKSGNKVAVTTTPFENTQSLV 1061
                             ||    972       982       992      1002      1012      1022      1032      1042      1052         
                             0|                                                                                                
                            965

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: PDZ domain-like (299)

Superfamily: PDZ domain-like (299)

Family: automated matches (94)

Protein domain: automated matches (94)

Human (Homo sapiens) [TaxId: 9606] (71)

1a	d3ps4a_	A:
1b	d3ps4b_	B:
1c	d3ps4c_	C:
1d	d3ps4d_	D:

(no "CATH Domain" information available for 3PS4)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PDZ-like (184)

Family: PDZ (172)

Homo sapiens (Human) (96)

1a	PDZ-3ps4D01	D:968-1052
1b	PDZ-3ps4D02	D:968-1052
1c	PDZ-3ps4D03	D:968-1052
1d	PDZ-3ps4D04	D:968-1052

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (MAST1_HUMAN | Q9Y2H9)

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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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: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:0004674	protein serine/threonine kinase activity	Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine 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:0007010	cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
	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:0018105	peptidyl-serine phosphorylation	The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	3ps4
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(no "Related Entries Specified in the PDB File" available for 3PS4)

Description

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Ligands, Modified Residues, Ions (2, 5)

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SS Bonds (0, 0)

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