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Theor.Model - manually (Jmol Viewer)

Theoretical Model (Jmol Viewer)

Title :   BIK

Authors :   Bhargavi Kondagari, Kalyan Chaitanya Pulipaka, Ramakrishna Annabhimoju, Uma Vuruputuri, K. Murthy Dwarkanath

Date :   12 Oct 06 (Deposition) - 24 Oct 06 (Release) - 24 Oct 06 (Revision)

Method :   THEORETICAL MODEL

Resolution :   NOT APPLICABLE

Chains :   Theor. Model : _

Keywords :   Bcl-2L13, Bcl Interacting Killer, Pro-Apoptotic Protein, Transmembrane Protein, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :

PubMed: search
(for further references see the PDB file header)

Molecule 1 - PROTEIN BCL-2L13 PRO-APOPTOTIC PROTEIN TRANSMEMBRANE PROTEIN
	Chains	:	_
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Other Details	:	B-CELL, LYMPH


Theoretical Model	:

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2IPE)

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

Theoretical Model

No.	Residues
1	Phe :45	-	Asp :46

Theoretical Model (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_029179	E	19	K	BIK_HUMAN	Polymorphism	4988415	_	E	19	K
2	UniProt	VAR_048420	T	26	I	BIK_HUMAN	Polymorphism	11090143	_	T	26	I
3	UniProt	VAR_029180	L	148	P	BIK_HUMAN	Polymorphism	11574527	_	L	148	P

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

Theoretical Model (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BH3	PS01259	Apoptosis regulator, Bcl-2 family BH3 motif signature.	BIK_HUMAN	57-71	1	_:57-71

Theoretical Model (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000216115	1	ENSE00001044574	chr22:43506754-43506809	56	BIK_HUMAN	-	0	0	-	-
1.2	ENST00000216115	2	ENSE00000880611	chr22:43520022-43520189	168	BIK_HUMAN	1-54	54	1	_:1-54	54
1.3	ENST00000216115	3	ENSE00000656749	chr22:43523703-43523801	99	BIK_HUMAN	54-87	34	1	_:54-87	34
1.4	ENST00000216115	4	ENSE00000656750	chr22:43524502-43524631	130	BIK_HUMAN	87-130	44	1	_:87-130	44
1.5	ENST00000216115	5	ENSE00000880612	chr22:43525219-43525718	500	BIK_HUMAN	131-160	30	1	_:131-160	30

Theoretical Model

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 _ from PDB  Type:PROTEIN  Length:160
 aligned with BIK_HUMAN | Q13323 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
            BIK_HUMAN     1 MSEVRPLSRDILMETLLYEQLLEPPTMEVLGMTDSEEDLDPMEDFDSLECMEGSDALALRLACIGDEMDVSLRAPRLAQLSEVAMHSLGLAFIYDQTEDIRDVLRSFMDGFTTLKENIMRFWRSPNPGSWVSCEQVLLALLLLLALLLPLLSGGLHLLLK 160
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh............hhhhhhhhhh..............eehhhhhhhhhhh....eeeeeeee.......hhhhheeeeeeee...hhhhhhhhhhh..................hhhhhhhhhh...........hhhhhh.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------K------I-------------------------------------------------------------------------------------------------------------------------P------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------BH3  PDB: -    ----------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: - UniProt: 1-54                        --------------------------------Exon 1.4  PDB: - UniProt: 87-130            Exon 1.5  PDB: -               Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------Exon 1.3  PDB: - UniProt: 54-87   ------------------------------------------------------------------------- Transcript 1 (2)
                 2ipe _   1 MSEVRPLSRDILMETLLYEQLLEPPTMEVLGMTDSEEDLDPMEDFDSLECMEGSDALALRLACIGDEMDVSLRAPRLAQLSEVAMHSLGLAFIYDQTEDIRDVLRSFMDGFTTLKENIMRFWRSPNPGSWVSCEQVLLALLLLLALLLPLLSGGLHLLLK 160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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 '\|'

(no "SCOP Domain" information available for 2IPE)

(no "CATH Domain" information available for 2IPE)

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

Theoretical Model(hide GO term definitions)

Chain (BIK_HUMAN | Q13323)

molecular function
	GO:0051400	BH domain binding	Interacting selectively and non-covalently with the Bcl-2 homology (BH) domain of a protein. Bcl-2-related proteins share homology in one to four conserved regions designated the Bcl-2 homology (BH) domains BH1, BH2, BH3 and BH4. These domains contribute at multiple levels to the function of these proteins in cell death and survival. Anti-apoptotic members of the Bcl-2 family have four BH domains (BH1-BH4). Pro-apoptotic members have fewer BH domains.
	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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0008637	apoptotic mitochondrial changes	The morphological and physiological alterations undergone by mitochondria during apoptosis.
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0008584	male gonad development	The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
	GO:0032464	positive regulation of protein homooligomerization	Any process that activates or increases the frequency, rate or extent of protein homooligomerization.
	GO:0090200	positive regulation of release of cytochrome c from mitochondria	Any process that increases the rate, frequency or extent of release of cytochrome c from mitochondria, the process in which cytochrome c is enabled to move from the mitochondrial intermembrane space into the cytosol, which is an early step in apoptosis and leads to caspase activation.
	GO:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
	GO:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
cellular component
	GO:0012505	endomembrane system	A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005740	mitochondrial envelope	The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm; includes the intermembrane space.
	GO:0031966	mitochondrial membrane	Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Theoretical Model
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	Sites
(no "Sites" information available for 2ipe)

	Cis Peptide Bonds
		Phe :45 - Asp :46	[ RasMol ]

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	BIK_HUMAN \| Q13323
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

PROSITE Motifs (1, 1)

Exons (4, 4)

Sequences/Alignments

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SCOP Domains (0, 0)

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Gene Ontology (16, 16)

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