3P1I - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   LIGAND BINDING DOMAIN OF HUMAN EPHRIN TYPE-B RECEPTOR 3

Authors :   J. R. Walker, L. Yermekbayeva, A. Seitova, J. Kania, C. Bountra, J. Weig C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon, Struct Genomics Consortium (Sgc)

Date :   30 Sep 10 (Deposition) - 19 Jan 11 (Release) - 19 Jan 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Atp-Binding, Kinase, Nucleotide-Binding, Receptor, Transferase, Phosphorylation, Transmembrane, Tyrosine-Protein Kinase, Glycoprotein, Structural Genomics Consortium, Sgc, Membrane, Single- Pass Type I Membrane Protein, Transferase, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Walker, L. Yermekbayeva, A. Seitova, J. Kania, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon
Ligand Binding Domain Of Human Ephb3
To Be Published
PubMed: search

Molecule 1 - EPHRIN TYPE-B RECEPTOR 3
	Chains	:	A, B, C
	EC Number	:	2.7.10.1
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Plasmid	:	PFHMSP-LIC-C
	Expression System Strain	:	SF9
	Expression System Taxid	:	7108
	Expression System Vector Type	:	PLASMID
	Fragment	:	LIGAND BINDING DOMAIN (UNP RESIDUES 39-211)
	Gene	:	EPHB3, ETK2, HEK2, TYR06, TYRO6
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	EPH-LIKE KINASE 2, EK2, HEK2, TYROSINE-PROTEIN KINASE TYRO6

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR B:49 , SER B:50	BINDING SITE FOR RESIDUE CL B 0
2	AC2	SOFTWARE	LYS B:177 , ARG B:179	BINDING SITE FOR RESIDUE SO4 B 1
3	AC3	SOFTWARE	LYS A:127 , ASN A:131 , GLN A:196	BINDING SITE FOR RESIDUE SO4 A 2

Asymmetric Unit

No.	Residues
1	A:81	-	A:199
2	A:116	-	A:126
3	B:81	-	B:199
4	B:116	-	B:126
5	C:81	-	C:199
6	C:116	-	C:126

Asymmetric Unit

No.	Residues
1	His A:57	-	Pro A:58
2	Gly A:182	-	Pro A:183
3	His B:57	-	Pro B:58
4	Gly B:182	-	Pro B:183
5	His C:57	-	Pro C:58
6	Gly C:182	-	Pro C:183

(no "SAP(SNP)/Variant" information available for 3P1I)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EPH_LBD	PS51550	Eph receptor ligand-binding domain profile.	EPHB3_HUMAN	39-217	3	A:39-211 B:39-210 C:39-210
2	RECEPTOR_TYR_KIN_V_1	PS00790	Receptor tyrosine kinase class V signature 1.	EPHB3_HUMAN	193-213	3	A:193-211 B:193-210 C:193-210

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EPH_LBD	PS51550	Eph receptor ligand-binding domain profile.	EPHB3_HUMAN	39-217	1	A:39-211 - -
2	RECEPTOR_TYR_KIN_V_1	PS00790	Receptor tyrosine kinase class V signature 1.	EPHB3_HUMAN	193-213	1	A:193-211 - -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EPH_LBD	PS51550	Eph receptor ligand-binding domain profile.	EPHB3_HUMAN	39-217	1	- B:39-210 -
2	RECEPTOR_TYR_KIN_V_1	PS00790	Receptor tyrosine kinase class V signature 1.	EPHB3_HUMAN	193-213	1	- B:193-210 -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EPH_LBD	PS51550	Eph receptor ligand-binding domain profile.	EPHB3_HUMAN	39-217	1	- - C:39-210
2	RECEPTOR_TYR_KIN_V_1	PS00790	Receptor tyrosine kinase class V signature 1.	EPHB3_HUMAN	193-213	1	- - C:193-210

(no "Exon" information available for 3P1I)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:171
 aligned with EPHB3_HUMAN | P54753 from UniProtKB/Swiss-Prot  Length:998

    Alignment length:174
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207    
          EPHB3_HUMAN    38 LEETLMDTKWVTSELAWTSHPESGWEEVSGYDEAMNPIRTYQVCNVRESSQNNWLRTGFIWRRDVQRVYVELKFTVRDCNSIPNIPGSCKETFNLFYYEADSDVASASSPFWMENPYVKVDTIAPDESFSRLDAGRVNTKVRSFGPLSKAGFYLAFQDQGACMSLISVRAFYKK 211
               SCOP domains d3p1ia_ A: automated matches                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.hhh......eee.....eeeeee.....eeeeeee.........eeee...ee......eeeeeeeee.hhhhh..........eeeeeeee.................eeeeee.......---....eeeeeee......eeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -EPH_LBD  PDB: A:39-211 UniProt: 39-217                                                                                                                                        PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------RECEPTOR_TYR_KIN_V_ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p1i A  38 DEETLMDTKWVTSELAWTSHPESGWEEVSGYDEAMNPIRTYQVCNVRESSQNNWLRTGFIWRRDVQRVYVELKFTVRDCNSIPNIPGSCKETFNLFYYEADSDVASASSPFWMENPYVKVDTIAPDESFS---AGRVNTKVRSFGPLSKAGFYLAFQDQGACMSLISVRAFYKK 211
                                    47        57        67        77        87        97       107       117       127       137       147       157       167   |   177       187       197       207    
                                                                                                                                                           167 171

Chain B from PDB  Type:PROTEIN  Length:164
 aligned with EPHB3_HUMAN | P54753 from UniProtKB/Swiss-Prot  Length:998

    Alignment length:172
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208  
          EPHB3_HUMAN    39 EETLMDTKWVTSELAWTSHPESGWEEVSGYDEAMNPIRTYQVCNVRESSQNNWLRTGFIWRRDVQRVYVELKFTVRDCNSIPNIPGSCKETFNLFYYEADSDVASASSPFWMENPYVKVDTIAPDESFSRLDAGRVNTKVRSFGPLSKAGFYLAFQDQGACMSLISVRAFYK 210
               SCOP domains d3p1ib_ B: automated matches                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhh......eee.....eeeeee.....eeeeeee.........eeee...ee......eeeeeeeee.hhhhh..........eeeeeeee.................eeeeee....--------..eeeeeee......eeeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) EPH_LBD  PDB: B:39-210 UniProt: 39-217                                                                                                                                       PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------RECEPTOR_TYR_KIN_V PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p1i B  39 EETLMDTKWVTSELAWTSHPESGWEEVSGYDEAMNPIRTYQVCNVRESSQNNWLRTGFIWRRDVQRVYVELKFTVRDCNSIPNIPGSCKETFNLFYYEADSDVASASSPFWMENPYVKVDTIAPDE--------RVNTKVRSFGPLSKAGFYLAFQDQGACMSLISVRAFYK 210
                                    48        58        68        78        88        98       108       118       128       138       148       158     |   -    |  178       188       198       208  
                                                                                                                                                       164      173

Chain C from PDB  Type:PROTEIN  Length:167
 aligned with EPHB3_HUMAN | P54753 from UniProtKB/Swiss-Prot  Length:998

    Alignment length:172
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208  
          EPHB3_HUMAN    39 EETLMDTKWVTSELAWTSHPESGWEEVSGYDEAMNPIRTYQVCNVRESSQNNWLRTGFIWRRDVQRVYVELKFTVRDCNSIPNIPGSCKETFNLFYYEADSDVASASSPFWMENPYVKVDTIAPDESFSRLDAGRVNTKVRSFGPLSKAGFYLAFQDQGACMSLISVRAFYK 210
               SCOP domains d3p1ic_ C: automated matches                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Ephrin_lbd-3p1iC01 C:39-210                                                                                                                                                  Pfam domains (1)
           Pfam domains (2) Ephrin_lbd-3p1iC02 C:39-210                                                                                                                                                  Pfam domains (2)
           Pfam domains (3) Ephrin_lbd-3p1iC03 C:39-210                                                                                                                                                  Pfam domains (3)
         Sec.struct. author .eeeee.hhh......eee.....eeeeee.....eeeeeee.........eeee...ee......eeeeeeeee.hhhhh..........eeeeeeee.................eeeeee......-----...eeeeeee......eeeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) EPH_LBD  PDB: C:39-210 UniProt: 39-217                                                                                                                                       PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------RECEPTOR_TYR_KIN_V PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p1i C  39 EETLMDTKWVTSELAWTSHPESGWEEVSGYDEAMNPIRTYQVCNVRESSQNNWLRTGFIWRRDVQRVYVELKFTVRDCNSIPNIPGSCKETFNLFYYEADSDVASASSPFWMENPYVKVDTIAPDESF-----GRVNTKVRSFGPLSKAGFYLAFQDQGACMSLISVRAFYK 210
                                    48        58        68        78        88        98       108       118       128       138       148       158       | -   |   178       188       198       208  
                                                                                                                                                         166   172

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: All beta proteins (24004)

Fold: Galactose-binding domain-like (314)

Superfamily: Galactose-binding domain-like (314)

Family: Ephrin receptor ligand binding domain (15)

Protein domain: automated matches (9)

Human (Homo sapiens) [TaxId: 9606] (9)

1a	d3p1ia_	A:
1b	d3p1ib_	B:
1c	d3p1ic_	C:

(no "CATH Domain" information available for 3P1I)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GBD (153)

Family: Ephrin_lbd (12)

Homo sapiens (Human) (9)

1a	Ephrin_lbd-3p1iC01	C:39-210
1b	Ephrin_lbd-3p1iC02	C:39-210
1c	Ephrin_lbd-3p1iC03	C:39-210

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (EPHB3_HUMAN | P54753)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0008046	axon guidance receptor activity	Combining with an extracellular messenger and transmitting the signal from one side of the membrane to the other to results in a change in cellular activity involved in axon guidance.
	GO:0005003	ephrin receptor activity	Combining with an ephrin to initiate a change in cell activity.
	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:0004672	protein kinase activity	Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
	GO:0004713	protein tyrosine kinase activity	Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
	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.
	GO:0004714	transmembrane receptor protein tyrosine kinase activity	Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate.
biological process
	GO:0001525	angiogenesis	Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
	GO:0007411	axon guidance	The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
	GO:0007413	axonal fasciculation	The collection of axons into a bundle of rods, known as a fascicle.
	GO:0016477	cell migration	The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
	GO:0021952	central nervous system projection neuron axonogenesis	Generation of a long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells in a different central nervous system region.
	GO:0022038	corpus callosum development	The process whose specific outcome is the progression of the corpus callosum over time, from its formation to the mature structure. The corpus callosum is a thick bundle of nerve fibers comprising a commissural plate connecting the two cerebral hemispheres. It consists of contralateral axon projections that provide communication between the right and left cerebral hemispheres.
	GO:0060996	dendritic spine development	The process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
	GO:0060997	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:0048546	digestive tract morphogenesis	The process in which the anatomical structures of the digestive tract are generated and organized. The digestive tract is the anatomical structure through which food passes and is processed.
	GO:0048013	ephrin receptor signaling pathway	The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0007399	nervous system development	The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
	GO:0060021	palate development	The biological process whose specific outcome is the progression of the palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The palate is the partition that separates the nasal and oral cavities.
	GO:0018108	peptidyl-tyrosine phosphorylation	The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
	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:0051965	positive regulation of synapse assembly	Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
	GO:0046777	protein autophosphorylation	The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0043087	regulation of GTPase activity	Any process that modulates the rate of GTP hydrolysis by a GTPase.
	GO:0050770	regulation of axonogenesis	Any process that modulates the frequency, rate or extent of axonogenesis, the generation of an axon, the long process of a neuron.
	GO:0022407	regulation of cell-cell adhesion	Any process that modulates the frequency, rate or extent of attachment of a cell to another cell.
	GO:0031290	retinal ganglion cell axon guidance	The process in which the migration of an axon growth cone of a retinal ganglion cell (RGC) is directed to its target in the brain in response to a combination of attractive and repulsive cues.
	GO:0034446	substrate adhesion-dependent cell spreading	The morphogenetic process that results in flattening of a cell as a consequence of its adhesion to a substrate.
	GO:0048538	thymus development	The process whose specific outcome is the progression of the thymus over time, from its formation to the mature structure. The thymus is a symmetric bi-lobed organ involved primarily in the differentiation of immature to mature T cells, with unique vascular, nervous, epithelial, and lymphoid cell components.
	GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0001655	urogenital system development	The process whose specific outcome is the progression of the urogenital system over time, from its formation to the mature structure.
cellular component
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	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:0030425	dendrite	A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	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:0005887	integral component of plasma membrane	The component of the plasma 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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	EPHB3_HUMAN \| P54753	:	3zfy 5l6o 5l6p

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