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Description

Title :   CRYSTAL STRUCTURE OF THE PEPP1 PLECKSTRIN HOMOLOGY DOMAIN IN COMPLEX WITH INOSITOL 1,3,4,5-TETRAKISPHOSPHATE

Authors :   C. C. Milburn, D. Komander, M. Deak, D. R. Alessi, D. M. F. Van Aalten

Date :   10 Oct 03 (Deposition) - 20 Oct 04 (Release) - 07 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.27

Chains :   Asym./Biol. Unit : A

Keywords :   Signaling Protein, Signal Transduction, Phosphoinositide Binding Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. C. Milburn, D. Komander, M. Deak, D. R. Alessi, D. M. F. Van Aalten
Crystal Structure Of The Pleckstrin Homology Domain Of Pepp
To Be Published
PubMed: search

Compounds

Molecule 1 - PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING FAMILY A MEMBER 4
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX4-T1
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Fragment	:	PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 45-167
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PEPP1, PH DOMAIN-CONTAINING FAMILY A MEMBER 4,

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 1)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	4IP	1	Ligand/Ion	INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE

Sites (1, 1)

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:1063 , ASP A:1065 , SER A:1066 , LYS A:1073 , ARG A:1075 , TYR A:1086 , LYS A:1088 , ARG A:1129 , ARG A:1146 , HOH A:2029	BINDING SITE FOR RESIDUE 4IP A2154

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (1, 1)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PH_DOMAIN	PS50003	PH domain profile.	PKHA4_HUMAN	54-153	1	A:1054-1153

Exons (4, 4)

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000263265	1	ENSE00001422227	chr19:49371858-49371340	519	PKHA4_HUMAN	-	0	0	-	-
1.2	ENST00000263265	2	ENSE00000718344	chr19:49370883-49370794	90	PKHA4_HUMAN	1-28	28	0	-	-
1.3	ENST00000263265	3	ENSE00000718336	chr19:49368867-49368760	108	PKHA4_HUMAN	29-64	36	1	A:1047-1064	18
1.4	ENST00000263265	4	ENSE00000853366	chr19:49364949-49364877	73	PKHA4_HUMAN	65-89	25	1	A:1065-1089	25
1.5	ENST00000263265	5	ENSE00000853365	chr19:49364758-49364658	101	PKHA4_HUMAN	89-122	34	1	A:1089-1122	34
1.6	ENST00000263265	6	ENSE00000718312	chr19:49363716-49363607	110	PKHA4_HUMAN	123-159	37	1	A:1123-1153	31
1.7	ENST00000263265	7	ENSE00000853364	chr19:49362941-49362726	216	PKHA4_HUMAN	159-231	73	0	-	-
1.8	ENST00000263265	8	ENSE00001130298	chr19:49362396-49362117	280	PKHA4_HUMAN	231-324	94	0	-	-
1.9	ENST00000263265	9	ENSE00000853362	chr19:49360753-49360679	75	PKHA4_HUMAN	325-349	25	0	-	-
1.10	ENST00000263265	10	ENSE00000954897	chr19:49357521-49357474	48	PKHA4_HUMAN	350-365	16	0	-	-
1.11	ENST00000263265	11	ENSE00000718302	chr19:49357344-49357264	81	PKHA4_HUMAN	366-392	27	0	-	-
1.12	ENST00000263265	12	ENSE00000718297	chr19:49357088-49356939	150	PKHA4_HUMAN	393-442	50	0	-	-
1.13	ENST00000263265	13	ENSE00000718291	chr19:49355583-49355485	99	PKHA4_HUMAN	443-475	33	0	-	-
1.14	ENST00000263265	14	ENSE00001233909	chr19:49351297-49351157	141	PKHA4_HUMAN	476-522	47	0	-	-
1.15	ENST00000263265	15	ENSE00001233902	chr19:49348873-49348774	100	PKHA4_HUMAN	523-556	34	0	-	-
1.16	ENST00000263265	16	ENSE00001233897	chr19:49348703-49348627	77	PKHA4_HUMAN	556-581	26	0	-	-
1.17	ENST00000263265	17	ENSE00001233890	chr19:49344567-49344406	162	PKHA4_HUMAN	582-635	54	0	-	-
1.18	ENST00000263265	18	ENSE00001233882	chr19:49342520-49342462	59	PKHA4_HUMAN	636-655	20	0	-	-
1.19	ENST00000263265	19	ENSE00001640853	chr19:49341386-49341274	113	PKHA4_HUMAN	655-693	39	0	-	-
1.20	ENST00000263265	20	ENSE00001619444	chr19:49340808-49340355	454	PKHA4_HUMAN	693-779	87	0	-	-

Sequences/Alignments

Asymmetric/Biological 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:107
 aligned with PKHA4_HUMAN | Q9H4M7 from UniProtKB/Swiss-Prot  Length:779

    Alignment length:107
                                    56        66        76        86        96       106       116       126       136       146       
         PKHA4_HUMAN     47 LRRDPNLPVHIRGWLHKQDSSGLRLWKRRWFVLSGHCLFYYKDSREESVLGSVLLPSYNIRPDGPGAPRGRRFTFTAEHPGMRTYVLAADTLEDLRGWLRALGRASR  153
               SCOP domains d1upra_ A: Phosphoinositol 3-phosphate binding protein-1, PEPP1                                             SCOP domains
               CATH domains 1uprA00 A:1047-1153 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)             CATH domains
               Pfam domains --------PH-1uprA01 A:1055-1153                                                                              Pfam domains
         Sec.struct. author ..........eeeeeeee.......eeeeeeeee..eeeee.........eeee.hhheeee...........eeeee......eeee..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------PH_DOMAIN  PDB: A:1054-1153 UniProt: 54-153                                                          PROSITE
           Transcript 1 (1) Exon 1.3          Exon 1.4  PDB: A:1065-108---------------------------------Exon 1.6  PDB: A:1123-1153      Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------Exon 1.5  PDB: A:1089-1122        ------------------------------- Transcript 1 (2)
                1upr A 1047 LRRDPNLPVHIRGWLHKQDSSGLRLWKRRWFVLSGHCLFYYKDSREESVLGSVLLPSYNIRPDGPGAPRGRRFTFTAEHPGMRTYVLAADTLEDLRGWLRALGRASR 1153
                                  1056      1066      1076      1086      1096      1106      1116      1126      1136      1146

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric/Biological 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: Pleckstrin-homology domain (PH domain) (102)

Protein domain: Phosphoinositol 3-phosphate binding protein-1, PEPP1 (2)

Human (Homo sapiens) [TaxId: 9606] (2)

d1upra_

CATH Domains (1, 1)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: PH-domain like (150)

Homologous Superfamily: Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) (147)

Human (Homo sapiens) (85)

1uprA00

A:1047-1153

Pfam Domains (1, 1)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PH (111)

Family: PH (71)

Homo sapiens (Human) (42)

PH-1uprA01

A:1055-1153

Gene Ontology (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PKHA4_HUMAN | Q9H4M7)

molecular function
	GO:0005545	1-phosphatidylinositol binding	Interacting selectively and non-covalently with phosphatidylinositol, any glycophospholipid with its sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
biological process
	GO:0008150	biological_process	Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Visualization

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	1upr
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Related Entries

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UniProtKB/Swiss-Prot
	PKHA4_HUMAN \| Q9H4M7	:	1upq

Related Entries Specified in the PDB File

1upq	CRYSTAL STRUCTURE OF THE PLECKSTRIN HOMOLOGY (PH) DOMAIN OF PEPP1