1BEH - JenaLib

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Title :   HUMAN PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN IN COMPLEX WITH CACODYLATE

Authors :   M. J. Banfield, J. J. Barker, A. Perry, R. L. Brady

Date :   14 May 98 (Deposition) - 16 Sep 98 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Lipid-Binding, Signalling, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Banfield, J. J. Barker, A. C. Perry, R. L. Brady
Function From Structure? The Crystal Structure Of Human Phosphatidylethanolamine-Binding Protein Suggests A Role In Membrane Signal Transduction.
Structure V. 6 1245 1998
PubMed-ID: 9782050 | Reference-DOI: 10.1016/S0969-2126(98)00125-7

Molecule 1 - PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN
	Cellular Location	:	CYTOPLASM, MEMBRANE-ASSOCIATED
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Plasmid	:	PET-15B
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	CAC	2	Ligand/Ion	CACODYLATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CAC	1	Ligand/Ion	CACODYLATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CAC	1	Ligand/Ion	CACODYLATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:70 , TRP A:84 , HIS A:86 , GLY A:110 , PRO A:111 , TYR A:120 , TYR A:181	BINDING SITE FOR RESIDUE CAC A 188
2	AC2	SOFTWARE	ASP B:70 , TRP B:84 , HIS B:86 , GLY B:110 , PRO B:111 , HIS B:118 , TYR B:120 , TYR B:181	BINDING SITE FOR RESIDUE CAC B 188

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

Asymmetric Unit

No.	Residues
1	Ala A:73	-	Pro A:74
2	Arg A:82	-	Glu A:83
3	Ala B:73	-	Pro B:74
4	Arg B:82	-	Glu B:83

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_006048	S	9	N	PEBP1_HUMAN	Polymorphism	---	A/B	S	9	N

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_006048	S	9	N	PEBP1_HUMAN	Polymorphism	---	A	S	9	N

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_006048	S	9	N	PEBP1_HUMAN	Polymorphism	---	B	S	9	N

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PBP	PS01220	Phosphatidylethanolamine-binding protein family signature.	PEBP1_HUMAN	64-86	2	A:64-86 B:64-86

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PBP	PS01220	Phosphatidylethanolamine-binding protein family signature.	PEBP1_HUMAN	64-86	1	A:64-86 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PBP	PS01220	Phosphatidylethanolamine-binding protein family signature.	PEBP1_HUMAN	64-86	1	- B:64-86

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000261313	1a	ENSE00000940085	chr12:118573870-118574149	280	PEBP1_HUMAN	1-45	45	2	A:3-45 B:4-45	43 42
1.2	ENST00000261313	2	ENSE00000755834	chr12:118575844-118575953	110	PEBP1_HUMAN	46-82	37	2	A:46-82 B:46-82	37 37
1.3	ENST00000261313	3	ENSE00000918093	chr12:118577256-118577356	101	PEBP1_HUMAN	82-116	35	2	A:82-116 B:82-116	35 35
1.4b	ENST00000261313	4b	ENSE00001141259	chr12:118582391-118583387	997	PEBP1_HUMAN	116-187	72	2	A:116-186 B:116-186	71 71

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:184
 aligned with PEBP1_HUMAN | P30086 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:184
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182    
          PEBP1_HUMAN     3 VDLSKWSGPLSLQEVDEQPQHPLHVTYAGAAVDELGKVLTPTQVKNRPTSISWDGLDSGKLYTLVLTDPDAPSRKDPKYREWHHFLVVNMKGNDISSGTVLSDYVGSGPPKGTGLHRYVWLVYEQDRPLKCDEPILSNRSGDHRGKFKVASFRKKYELRAPVAGTCYQAEWDDYVPKLYEQLSG 186
               SCOP domains d1beha_ A: Phosphatidylethanolamine binding protein, PEBP                                                                                                                                SCOP domains
               CATH domains 1behA00 A:3-186 Phosphatidylethanolamine-binding Protein;                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh...............eeeee..eee.................eeee........eeeeeee...............eeeeee..........................eeeeeeeee........................hhhhhhhh......eeeeeee....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------N--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------PBP  PDB: A:64-86      ---------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:3-45 UniProt: 1-45       Exon 1.2  PDB: A:46-82 UniProt: 46-82---------------------------------Exon 1.4b  PDB: A:116-186 UniProt: 116-187 [INCOMPLETE]                 Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------Exon 1.3  PDB: A:82-116            ---------------------------------------------------------------------- Transcript 1 (2)
                 1beh A   3 VDLSKWSGPLSLQEVDEQPQHPLHVTYAGAAVDELGKVLTPTQVKNRPTSISWDGLDSGKLYTLVLTDPDAPSRKDPKYREWHHFLVVNMKGNDISSGTVLSDYVGSGPPKGTGLHRYVWLVYEQDRPLKCDEPILSNRSGDHRGKFKVASFRKKYELRAPVAGTCYQAEWDDYVPKLYEQLSG 186
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain B from PDB  Type:PROTEIN  Length:183
 aligned with PEBP1_HUMAN | P30086 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:183
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183   
          PEBP1_HUMAN     4 DLSKWSGPLSLQEVDEQPQHPLHVTYAGAAVDELGKVLTPTQVKNRPTSISWDGLDSGKLYTLVLTDPDAPSRKDPKYREWHHFLVVNMKGNDISSGTVLSDYVGSGPPKGTGLHRYVWLVYEQDRPLKCDEPILSNRSGDHRGKFKVASFRKKYELRAPVAGTCYQAEWDDYVPKLYEQLSG 186
               SCOP domains d1behb_ B: Phosphatidylethanolamine binding protein, PEBP                                                                                                                               SCOP domains
               CATH domains 1behB00 B:4-186 Phosphatidylethanolamine-binding Protein;                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhh...............eeeee..eee.................eeee........eeeeeee...............eeeeee..........................eeeeeeeee........................hhhhhhhh......eeeeeee....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----N--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------PBP  PDB: B:64-86      ---------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: B:4-45 UniProt: 1-45      Exon 1.2  PDB: B:46-82 UniProt: 46-82---------------------------------Exon 1.4b  PDB: B:116-186 UniProt: 116-187 [INCOMPLETE]                 Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------Exon 1.3  PDB: B:82-116            ---------------------------------------------------------------------- Transcript 1 (2)
                 1beh B   4 DLSKWSGPLSLQEVDEQPQHPLHVTYAGAAVDELGKVLTPTQVKNRPTSISWDGLDSGKLYTLVLTDPDAPSRKDPKYREWHHFLVVNMKGNDISSGTVLSDYVGSGPPKGTGLHRYVWLVYEQDRPLKCDEPILSNRSGDHRGKFKVASFRKKYELRAPVAGTCYQAEWDDYVPKLYEQLSG 186
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: PEBP-like (18)

Superfamily: PEBP-like (18)

Family: Phosphatidylethanolamine binding protein (12)

Protein domain: Phosphatidylethanolamine binding protein, PEBP (6)

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

1a	d1beha_	A:
1b	d1behb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Phosphatidylethanolamine-binding Protein (16)

Homologous Superfamily: Phosphatidylethanolamine-binding Protein; (16)

Human (Homo sapiens) (2)

1a	1behB00	B:4-186
1b	1behA00	A:3-186

(no "Pfam Domain" information available for 1BEH)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PEBP1_HUMAN | P30086)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	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:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	GO:0008429	phosphatidylethanolamine binding	Interacting selectively and non-covalently with phosphatidylethanolamine, any of a class of glycerophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of ethanolamine.
	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:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:0004867	serine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
	GO:0000165	MAPK cascade	An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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.

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		Arg A:82 - Glu A:83	[ RasMol ]
		Arg B:82 - Glu B:83	[ RasMol ]

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	1beh
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	PEBP1_HUMAN \| P30086	:	1bd9 2l7w 2qyq

(no "Related Entries Specified in the PDB File" available for 1BEH)

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

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Exons (4, 8)

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