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Description

Title :   SOLUTION STRUCTURE OF THE PH DOMAIN OF PEPP-3 FROM HUMAN

Authors :   H. Li, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   13 Dec 05 (Deposition) - 13 Jun 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Ph Domain, Pepp-3, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Li, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Ph Domain Of Pepp-3 From Human
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING PROTEIN FAMILY A MEMBER 6
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P050711-08
	Expression System Vector Type	:	PLASMID
	Fragment	:	PH DOMAIN
	Gene	:	PLEKHA6
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	PHOSPHOINOSITOL 3-PHOSPHATE-BINDING PROTEIN 3, PEPP-3

Structural Features

Chains, Units


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2D9Y)

Sites (0, 0)

(no "Site" information available for 2D9Y)

SS Bonds (0, 0)

(no "SS Bond" information available for 2D9Y)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2D9Y)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2D9Y)

PROSITE Motifs (1, 1)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PH_DOMAIN	PS50003	PH domain profile.	PKHA6_HUMAN	59-158	1	A:10-109

Exons (4, 4)

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000272203	1	ENSE00001379233	chr1:204329044-204328822	223	PKHA6_HUMAN	-	0	0	-	-
1.2	ENST00000272203	2	ENSE00001365727	chr1:204243937-204243857	81	PKHA6_HUMAN	-	0	0	-	-
1.3a	ENST00000272203	3a	ENSE00001125876	chr1:204242868-204242754	115	PKHA6_HUMAN	1-34	34	0	-	-
1.4	ENST00000272203	4	ENSE00000962329	chr1:204237440-204237336	105	PKHA6_HUMAN	35-69	35	1	A:1-20 (gaps)	24
1.5	ENST00000272203	5	ENSE00000962330	chr1:204236675-204236603	73	PKHA6_HUMAN	70-94	25	1	A:21-45	25
1.6	ENST00000272203	6	ENSE00000962331	chr1:204234170-204234070	101	PKHA6_HUMAN	94-127	34	1	A:45-78	34
1.8c	ENST00000272203	8c	ENSE00000962332	chr1:204230576-204230434	143	PKHA6_HUMAN	128-175	48	1	A:79-117	39
1.9	ENST00000272203	9	ENSE00000962333	chr1:204228868-204228386	483	PKHA6_HUMAN	175-336	162	0	-	-
1.10a	ENST00000272203	10a	ENSE00000962334	chr1:204226997-204226481	517	PKHA6_HUMAN	336-508	173	0	-	-
1.14	ENST00000272203	14	ENSE00000962335	chr1:204219742-204219674	69	PKHA6_HUMAN	509-531	23	0	-	-
1.15b	ENST00000272203	15b	ENSE00000962336	chr1:204218392-204218312	81	PKHA6_HUMAN	532-558	27	0	-	-
1.16	ENST00000272203	16	ENSE00000962337	chr1:204218098-204217949	150	PKHA6_HUMAN	559-608	50	0	-	-
1.17	ENST00000272203	17	ENSE00000962338	chr1:204216588-204216493	96	PKHA6_HUMAN	609-640	32	0	-	-
1.18	ENST00000272203	18	ENSE00000962339	chr1:204214854-204214743	112	PKHA6_HUMAN	641-678	38	0	-	-
1.19	ENST00000272203	19	ENSE00000962340	chr1:204214131-204213992	140	PKHA6_HUMAN	678-724	47	0	-	-
1.20	ENST00000272203	20	ENSE00000962341	chr1:204210942-204210813	130	PKHA6_HUMAN	725-768	44	0	-	-
1.21	ENST00000272203	21	ENSE00000962342	chr1:204210609-204210503	107	PKHA6_HUMAN	768-803	36	0	-	-
1.22	ENST00000272203	22	ENSE00001039740	chr1:204199714-204199541	174	PKHA6_HUMAN	804-861	58	0	-	-
1.23	ENST00000272203	23	ENSE00001039735	chr1:204198232-204198065	168	PKHA6_HUMAN	862-917	56	0	-	-
1.24	ENST00000272203	24	ENSE00001039739	chr1:204197989-204197856	134	PKHA6_HUMAN	918-962	45	0	-	-
1.25	ENST00000272203	25	ENSE00001039741	chr1:204197356-204197211	146	PKHA6_HUMAN	962-1011	50	0	-	-
1.26b	ENST00000272203	26b	ENSE00001125867	chr1:204192713-204192590	124	PKHA6_HUMAN	1011-1048	38	0	-	-
1.27	ENST00000272203	27	ENSE00001801942	chr1:204191907-204190349	1559	PKHA6_HUMAN	-	0	0	-	-

Sequences/Alignments

NMR Structure

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
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Chain A from PDB  Type:PROTEIN  Length:117
 aligned with PKHA6_HUMAN | Q9Y2H5 from UniProtKB/Swiss-Prot  Length:1048

    Alignment length:121
                                    55        65        75        85        95       105       115       125       135       145       155       165 
          PKHA6_HUMAN    46 GKRSHSMKRNPNAPVTKAGWLFKQASSGVKQWNKRWFVLVDRCLFYYKDEKEESILGSIPLLSFRVAAVQPSDNISRKHTFKAEHAGVRTYFFSAESPEEQEAWIQAMGEAARVQIPPAQK 166
               SCOP domains d2d9ya_     A: automated matches                                                                                          SCOP domains
               CATH domains 2d9yA00     A:1-117 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......----.....eeeeeeee.......eeeeeeeee..eeeee.........eeee....eeee...........eeeee.....eeeee...hhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------PH_DOMAIN  PDB: A:10-109 UniProt: 59-158                                                            -------- PROSITE
           Transcript 1 (1) Exon 1.4 UniProt: 35-69 Exon 1.5  PDB: A:21-45   ---------------------------------Exon 1.8c  PDB: A:79-117 [INCOMPLETE]   Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------Exon 1.6  PDB: A:45-78            --------------------------------------- Transcript 1 (2)
                 2d9y A   1 GSSGSSG----NAPVTKAGWLFKQASSGVKQWNKRWFVLVDRCLFYYKDEKEESILGSIPLLSFRVAAVQPSDNISRKHTFKAEHAGVRTYFFSAESPEEQEAWIQAMGEAARVQSGPSSG 117
                                  |  - |      16        26        36        46        56        66        76        86        96       106       116 
                                  7    8

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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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: PH domain-like barrel (258)

Superfamily: PH domain-like (257)

Family: automated matches (50)

Protein domain: automated matches (50)

Human (Homo sapiens) [TaxId: 9606] (30)

d2d9ya_

CATH Domains (1, 1)

NMR Structure

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)

2d9yA00

A:1-117

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2D9Y)

Gene Ontology (0, 0)

NMR Structure(hide GO term definitions)

(no "Gene Ontology" information available for 2D9Y)

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2d9y)

Still Images

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Related Entries

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	PKHA6_HUMAN \| Q9Y2H5	:	2yry

Related Entries Specified in the PDB File

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