1W2D - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   HUMAN INOSITOL (1,4,5)-TRISPHOSPHATE 3-KINASE COMPLEXED WITH MN2+/ADP/INS(1,3,4,5)P4

Authors :   B. Gonzalez, M. J. Schell, R. F. Irvine, R. L. Williams

Date :   01 Jul 04 (Deposition) - 09 Sep 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.94

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

Keywords :   Inositol Phosphate Kinase, Adp, Ip4, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Gonzalez, M. J. Schell, A. J. Letcher, D. B. Veprintsev, R. F. Irvine, R. L. Williams
Structure Of A Human Inositol 1, 4, 5-Trisphosphate 3-Kinase; Substrate Binding Reveals Why It Is Not A Phosphoinositide 3-Kinase
Mol. Cell V. 15 689 2004
PubMed-ID: 15350214 | Reference-DOI: 10.1016/J.MOLCEL.2004.08.004

Molecule 1 - INOSITOL-TRISPHOSPHATE 3-KINASE A
	Chains	:	A, B
	EC Number	:	2.1.7.127
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	C41
	Expression System Taxid	:	562
	Expression System Variant	:	DE3
	Expression System Vector	:	POPTG
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 197-461
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	INOSITOL 1,4,5-TRISPHOSPHATE 3-KINASE, IP3-3K

		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 (4, 9)

No.	Name	Count	Type	Full Name
1	4IP	2	Ligand/Ion	INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
2	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	MN	2	Ligand/Ion	MANGANESE (II) ION
4	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	4IP	1	Ligand/Ion	INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
2	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	4IP	1	Ligand/Ion	INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
2	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:416 , ADP A:1462 , 4IP A:1463 , HOH A:2105	BINDING SITE FOR RESIDUE MN A1464
2	AC2	SOFTWARE	ARG A:352 , SER A:457 , ARG A:461 , HOH A:2122	BINDING SITE FOR RESIDUE SO4 A1465
3	AC3	SOFTWARE	GLN A:354 , ARG A:357 , HOH A:2129	BINDING SITE FOR RESIDUE SO4 A1466
4	AC4	SOFTWARE	ASP B:416 , ADP B:1462 , 4IP B:1463 , HOH B:2129	BINDING SITE FOR RESIDUE MN B1464
5	AC5	SOFTWARE	GLN B:354 , ARG B:357 , HOH B:2130	BINDING SITE FOR RESIDUE SO4 B1465
6	AC6	SOFTWARE	SER A:197 , PHE A:198 , LYS A:209 , PRO A:232 , GLN A:249 , ASP A:250 , LEU A:251 , ASP A:262 , LYS A:336 , ASP A:416 , MN A:1464 , HOH A:2125 , HOH A:2126	BINDING SITE FOR RESIDUE ADP A1462
7	AC7	SOFTWARE	LYS A:264 , ARG A:285 , MET A:288 , LYS A:312 , TYR A:315 , MET A:316 , ARG A:319 , LYS A:419 , MN A:1464 , HOH A:2059 , HOH A:2127 , HOH A:2128	BINDING SITE FOR RESIDUE 4IP A1463
8	AC8	SOFTWARE	SER B:197 , PHE B:198 , LYS B:209 , GLN B:249 , ASP B:250 , LEU B:251 , ASP B:262 , LYS B:336 , LEU B:401 , ASP B:416 , MN B:1464 , HOH B:2125 , HOH B:2126 , HOH B:2127	BINDING SITE FOR RESIDUE ADP B1462
9	AC9	SOFTWARE	LYS B:264 , ARG B:285 , MET B:288 , LYS B:291 , LYS B:312 , TYR B:315 , MET B:316 , ARG B:319 , GLU B:333 , LYS B:419 , MN B:1464 , HOH B:2128	BINDING SITE FOR RESIDUE 4IP B1463

(no "SS Bond" information available for 1W2D)

(no "Cis Peptide Bond" information available for 1W2D)

(no "SAP(SNP)/Variant" information available for 1W2D)

(no "PROSITE Motif" information available for 1W2D)

Asymmetric Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000260386	2a	ENSE00001206292	chr15:41786059-41786614	556	IP3KA_HUMAN	1-163	163	0	-	-
1.3b	ENST00000260386	3b	ENSE00000931025	chr15:41793661-41793757	97	IP3KA_HUMAN	164-196	33	0	-	-
1.4a	ENST00000260386	4a	ENSE00000931026	chr15:41793833-41794049	217	IP3KA_HUMAN	196-268	73	2	A:197-268 B:197-268	72 72
1.5	ENST00000260386	5	ENSE00000931027	chr15:41794195-41794399	205	IP3KA_HUMAN	268-336	69	2	A:268-336 B:268-336 (gaps)	69 69
1.6b	ENST00000260386	6b	ENSE00000931028	chr15:41794600-41794701	102	IP3KA_HUMAN	337-370	34	2	A:337-370 B:337-370	34 34
1.7	ENST00000260386	7	ENSE00000931029	chr15:41794986-41795057	72	IP3KA_HUMAN	371-394	24	2	A:371-394 B:371-394	24 24
1.8b	ENST00000260386	8b	ENSE00000931030	chr15:41795161-41795749	589	IP3KA_HUMAN	395-461	67	2	A:395-461 B:395-461	67 67

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:265
 aligned with IP3KA_HUMAN | P23677 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:265
                                   206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456     
          IP3KA_HUMAN   197 SFKAAGTSGLILKRCSEPERYCLARLMADALRGCVPAFHGVVERDGESYLQLQDLLDGFDGPCVLDCKMGVRTYLEEELTKARERPKLRKDMYKKMLAVDPEAPTEEEHAQRAVTKPRYMQWREGISSSTTLGFRIEGIKKADGSCSTDFKTTRSREQVLRVFEEFVQGDEEVLRRYLNRLQQIRDTLEVSEFFRRHEVIGSSLLFVHDHCHRAGVWLIDFGKTTPLPDGQILDHRRPWEEGNREDGYLLGLDNLIGILASLAER 461
               SCOP domains d1w2da_ A: Inositol 1,4,5-trisphosphate 3-kinase A, IP3K A                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeeee.hhhhhhhhhhhhhhhhhhhh..eeeeee....eeeeee.........eeeeeee......hhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhh..hhhhhhhhhhhhhhhhhhheeeeeee.....ee.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhheeee..eeeeee.....eeeeee...eeee....................hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4a  PDB: A:197-268 UniProt: 196-268 [INCOMPLETE]                 --------------------------------------------------------------------Exon 1.6b  PDB: A:337-370         Exon 1.7  PDB: A:371-394Exon 1.8b  PDB: A:395-461 UniProt: 395-461                          Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------Exon 1.5  PDB: A:268-336 UniProt: 268-336                            ----------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1w2d A 197 SFKAAGTSGLILKRCSEPERYCLARLMADALRGCVPAFHGVVERDGESYLQLQDLLDGFDGPCVLDCKMGVRTYLEEELTKARERPKLRKDMYKKMLAVDPEAPTEEEHAQRAVTKPRYMQWREGISSSTTLGFRIEGIKKADGSCSTDFKTTRSREQVLRVFEEFVQGDEEVLRRYLNRLQQIRDTLEVSEFFRRHEVIGSSLLFVHDHCHRAGVWLIDFGKTTPLPDGQILDHRRPWEEGNREDGYLLGLDNLIGILASLAER 461
                                   206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456

Chain B from PDB  Type:PROTEIN  Length:250
 aligned with IP3KA_HUMAN | P23677 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:265
                                   206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456     
          IP3KA_HUMAN   197 SFKAAGTSGLILKRCSEPERYCLARLMADALRGCVPAFHGVVERDGESYLQLQDLLDGFDGPCVLDCKMGVRTYLEEELTKARERPKLRKDMYKKMLAVDPEAPTEEEHAQRAVTKPRYMQWREGISSSTTLGFRIEGIKKADGSCSTDFKTTRSREQVLRVFEEFVQGDEEVLRRYLNRLQQIRDTLEVSEFFRRHEVIGSSLLFVHDHCHRAGVWLIDFGKTTPLPDGQILDHRRPWEEGNREDGYLLGLDNLIGILASLAER 461
               SCOP domains d1w2db_ B: Inositol 1,4,5-trisphosphate 3-kinase A, IP3K A                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------IPK-1w2dB01 B:245-456                                                                                                                                                                                               ----- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------IPK-1w2dB02 B:245-456                                                                                                                                                                                               ----- Pfam domains (2)
         Sec.struct. author .eee.....eeeee.hhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeeee.........eeeeeee......hhhhhh.----...hhhhhhhhhhh.-----------..hhhhhhhhhhhhhhhhhhheeeeeee.....ee.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhheee...eeeeee.....eeeeee....eee....................hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4a  PDB: B:197-268 UniProt: 196-268 [INCOMPLETE]                 --------------------------------------------------------------------Exon 1.6b  PDB: B:337-370         Exon 1.7  PDB: B:371-394Exon 1.8b  PDB: B:395-461 UniProt: 395-461                          Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------Exon 1.5  PDB: B:268-336 (gaps) UniProt: 268-336                     ----------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1w2d B 197 SFKAAGTSGLILKRCSEPERYCLARLMADALRGCVPAFHGVVERDGESYLQLQDLLDGFDGPCVLDCKMGVRTYLEEELTKA----KLRKDMYKKMLAVDP-----------AVTKPRYMQWREGISSSTTLGFRIEGIKKADGSCSTDFKTTRSREQVLRVFEEFVQGDEEVLRRYLNRLQQIRDTLEVSEFFRRHEVIGSSLLFVHDHCHRAGVWLIDFGKTTPLPDGQILDHRRPWEEGNREDGYLLGLDNLIGILASLAER 461
                                   206       216       226       236       246       256       266       276 |    |286       296|        -  |    316       326       336       346       356       366       376       386       396       406       416       426       436       446       456     
                                                                                                           278  283           297         309

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(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: SAICAR synthase-like (28)

Superfamily: SAICAR synthase-like (28)

Family: Inositol polyphosphate kinase (IPK) (6)

Protein domain: Inositol 1,4,5-trisphosphate 3-kinase A, IP3K A (4)

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

1a	d1w2da_	A:
1b	d1w2db_	B:

(no "CATH Domain" information available for 1W2D)

Asymmetric Unit

Clans(

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Families(

)

Organisms( (-)

)

Clan: no clan defined [family: IPK] (3)

Family: IPK (3)

Homo sapiens (Human) (2)

1a	IPK-1w2dB01	B:245-456
1b	IPK-1w2dB02	B:245-456

Asymmetric Unit(hide GO term definitions)

Chain A,B (IP3KA_HUMAN | P23677)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0048365	Rac GTPase binding	Interacting selectively and non-covalently with Rac protein, any member of the Rac subfamily of the Ras superfamily of monomeric GTPases.
	GO:0005516	calmodulin binding	Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
	GO:0004683	calmodulin-dependent protein kinase activity	Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions require the presence of calcium-bound calmodulin.
	GO:0008440	inositol-1,4,5-trisphosphate 3-kinase activity	Catalysis of the reaction: 1D-myo-inositol 1,4,5-trisphosphate + ATP = 1D-myo-inositol 1,3,4,5-tetrakisphosphate + ADP + 2 H(+).
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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: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:0030036	actin 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 comprising actin filaments and their associated proteins.
	GO:0097062	dendritic spine maintenance	The organization process that preserves a dendritic spine in a stable functional or structural state. A dendritic spine is a specialized protrusion from a neuronal dendrite and is involved in synaptic transmission.
	GO:0006020	inositol metabolic process	The chemical reactions and pathways involving inositol, 1,2,3,4,5,6-cyclohexanehexol, a growth factor for animals and microorganisms.
	GO:0043647	inositol phosphate metabolic process	The chemical reactions and pathways involving inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached.
	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:0061003	positive regulation of dendritic spine morphogenesis	Any process that increases the rate, frequency, or extent of dendritic spine morphogenesis, the process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0048167	regulation of synaptic plasticity	A process that modulates synaptic plasticity, the ability of synapses to change as circumstances require. They may alter function, such as increasing or decreasing their sensitivity, or they may increase or decrease in actual numbers.
	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.
cellular component
	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:0043197	dendritic spine	A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.

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	1w2d
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	IP3KA_HUMAN \| P23677
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UniProtKB/Swiss-Prot
	IP3KA_HUMAN \| P23677	:	1w2c 1w2f 4upu

1w2c	HUMAN INOSITOL (1,4,5) TRISPHOSPHATE 3- KINASE COMPLEXED WITH MN2+/AMPPNP/INS(1,4,5)P3
1w2f	HUMAN INOSITOL (1,4,5)-TRISPHOSPHATE 3- KINASE SUBSTITUTED WITH SELENOMETHIONINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

SS Bonds (0, 0)

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Exons (5, 10)

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SCOP Domains (1, 2)

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