Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  EPHB2/SNEW ANTAGONISTIC PEPTIDE COMPLEX
 
Authors :  J. E. Chrencik, A. Brooun, M. I. Recht, G. Nicola, E. B. Pasquale, P. Kuhn, Accelerated Technologies Center For Gene To 3D Structure (Atcg3D)
Date :  18 Jun 07  (Deposition) - 06 Nov 07  (Release) - 08 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,D,P
Biol. Unit 1:  A,P  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  A,B,D,P  (1x)
Keywords :  Receptor Tyrosine Kinase, Bi-Directional Signaling, Tumorigenesis, Angiogenesis, Signaling Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Accelerated Technologies Center For Gene To 3D Structure, Atcg3D (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. E. Chrencik, A. Brooun, M. I. Recht, G. Nicola, L. K. Davis, R. Abagyan, H. Widmer, E. B. Pasquale, P. Kuhn
Three-Dimensional Structure Of The Ephb2 Receptor In Complex With An Antagonistic Peptide Reveals A Novel Mode Of Inhibition.
J. Biol. Chem. V. 282 36505 2007
PubMed-ID: 17897949  |  Reference-DOI: 10.1074/JBC.M706340200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EPHRIN TYPE-B RECEPTOR 2
    ChainsA, B
    EC Number2.7.10.1
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPBAC6
    Expression System StrainHI-5
    Expression System Taxid7108
    Expression System Vector TypePFASTBAC1
    FragmentEPHB2
    GeneEPHB2, DRT, EPHT3, EPTH3, ERK, HEK5, TYRO5
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTYROSINE-PROTEIN KINASE RECEPTOR EPH-3
 
Molecule 2 - ANTAGONISTIC PEPTIDE
    ChainsD, P
    EngineeredYES
    Other DetailsANTAGONISTIC PEPTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABDP
Biological Unit 1 (1x)A  P
Biological Unit 2 (1x) BD 
Biological Unit 3 (1x)ABDP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1SO412Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION
Biological Unit 3 (1, 12)
No.NameCountTypeFull Name
1SO412Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS B:95 , ARG B:203BINDING SITE FOR RESIDUE SO4 B 401
02AC2SOFTWAREARG B:88 , GLY B:90 , HIS B:92BINDING SITE FOR RESIDUE SO4 B 402
03AC3SOFTWAREMET B:32 , ASP B:33 , LEU B:41 , HOH B:470BINDING SITE FOR RESIDUE SO4 B 403
04AC4SOFTWAREPHE A:135 , PRO A:136 , ASN A:137 , PRO A:142 , HOH A:481BINDING SITE FOR RESIDUE SO4 A 404
05AC5SOFTWAREARG A:179 , HOH A:480 , ARG B:179BINDING SITE FOR RESIDUE SO4 A 405
06AC6SOFTWARESER A:55 , ARG A:65BINDING SITE FOR RESIDUE SO4 A 406
07AC7SOFTWAREPRO A:109 , SER A:110 , HOH B:441 , GLN D:6 , HOH D:285BINDING SITE FOR RESIDUE SO4 D 407
08AC8SOFTWAREARG A:88 , GLY A:90 , HIS A:92BINDING SITE FOR RESIDUE SO4 A 408
09AC9SOFTWARETHR B:36 , SER B:75 , SER B:76 , SER B:114BINDING SITE FOR RESIDUE SO4 B 409
10BC1SOFTWAREPRO B:109 , SER B:110 , GLN P:6 , HOH P:14BINDING SITE FOR RESIDUE SO4 B 410
11BC2SOFTWARETRP B:80 , TYR B:122 , MET B:139 , GLU B:140 , GLN B:187 , HOH B:453 , HOH B:491BINDING SITE FOR RESIDUE SO4 B 411
12BC3SOFTWARESER B:55 , ARG B:65BINDING SITE FOR RESIDUE SO4 B 412

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:70 -A:192
2A:105 -A:115
3B:70 -B:192
4B:105 -B:115

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1His A:46 -Pro A:47
2Phe A:135 -Pro A:136
3Gly A:161 -Gly A:162
4Gly A:175 -Pro A:176
5His B:46 -Pro B:47
6Phe B:135 -Pro B:136
7Gly B:175 -Pro B:176

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EPH_LBDPS51550 Eph receptor ligand-binding domain profile.EPHB2_HUMAN20-202
 
  2A:28-203
B:28-203
2RECEPTOR_TYR_KIN_V_1PS00790 Receptor tyrosine kinase class V signature 1.EPHB2_HUMAN178-198
 
  2A:186-203
B:186-203
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EPH_LBDPS51550 Eph receptor ligand-binding domain profile.EPHB2_HUMAN20-202
 
  1A:28-203
-
2RECEPTOR_TYR_KIN_V_1PS00790 Receptor tyrosine kinase class V signature 1.EPHB2_HUMAN178-198
 
  1A:186-203
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EPH_LBDPS51550 Eph receptor ligand-binding domain profile.EPHB2_HUMAN20-202
 
  1-
B:28-203
2RECEPTOR_TYR_KIN_V_1PS00790 Receptor tyrosine kinase class V signature 1.EPHB2_HUMAN178-198
 
  1-
B:186-203
Biological Unit 3 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EPH_LBDPS51550 Eph receptor ligand-binding domain profile.EPHB2_HUMAN20-202
 
  2A:28-203
B:28-203
2RECEPTOR_TYR_KIN_V_1PS00790 Receptor tyrosine kinase class V signature 1.EPHB2_HUMAN178-198
 
  2A:186-203
B:186-203

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000004001911aENSE00001464057chr1:23037458-2303753679EPHB2_HUMAN1-21212A:28-29
B:28-29
2
2
1.3ENST000004001913ENSE00001066292chr1:23107914-2310797865EPHB2_HUMAN21-42222A:29-50
B:29-50
22
22
1.4ENST000004001914ENSE00000955704chr1:23110885-23111569685EPHB2_HUMAN43-2712292A:51-203
B:51-203
153
153
1.6ENST000004001916ENSE00000955705chr1:23189530-23189685156EPHB2_HUMAN271-323530--
1.7aENST000004001917aENSE00000955706chr1:23191370-23191705336EPHB2_HUMAN323-4351130--
1.8aENST000004001918aENSE00000908689chr1:23208852-23208976125EPHB2_HUMAN435-476420--
1.10bENST0000040019110bENSE00000908690chr1:23219377-23219539163EPHB2_HUMAN477-531550--
1.11ENST0000040019111ENSE00000908691chr1:23221965-23222073109EPHB2_HUMAN531-567370--
1.12bENST0000040019112bENSE00000908692chr1:23222907-2322297165EPHB2_HUMAN567-589230--
1.13ENST0000040019113ENSE00000908693chr1:23232480-23232602123EPHB2_HUMAN589-630420--
1.14ENST0000040019114ENSE00000908694chr1:23233203-23233450248EPHB2_HUMAN630-712830--
1.15ENST0000040019115ENSE00001647153chr1:23234446-23234661216EPHB2_HUMAN713-784720--
1.16ENST0000040019116ENSE00001769046chr1:23235515-23235664150EPHB2_HUMAN785-834500--
1.17ENST0000040019117ENSE00000908697chr1:23236875-23237068194EPHB2_HUMAN835-899650--
1.18aENST0000040019118aENSE00000908698chr1:23238937-23239092156EPHB2_HUMAN899-951530--
1.18cENST0000040019118cENSE00001273135chr1:23239955-23240057103EPHB2_HUMAN951-985350--
1.18gENST0000040019118gENSE00001933590chr1:23240151-232418181668EPHB2_HUMAN986-1055700--

(-) Sequences/Alignments

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:176
 aligned with EPHB2_HUMAN | P29323 from UniProtKB/Swiss-Prot  Length:1055

    Alignment length:176
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189      
          EPHB2_HUMAN    20 EETLMDSTTATAELGWMVHPPSGWEEVSGYDENMNTIRTYQVCNVFESSQNNWLRTKFIRRRGAHRIHVEMKFSVRDCSSIPSVPGSCKETFNLYYYEADFDSATKTFPNWMENPWVKVDTIAADESFSQVDLGGRVMKINTEVRSFGPVSRSGFYLAFQDYGGCMSLIAVRVFYR 195
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qbxA00 A:28-203 Galactose-binding domain-like                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhh......eee.....eeeeee.....eeeeeee.........eeee...ee......eeeeeeeee.hhhhh..........eeeeeeee.................eeeeee......eeeee..eeeeeeeeeeee......eeeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) EPH_LBD  PDB: A:28-203 UniProt: 20-202                                                                                                                                           PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------RECEPTOR_TYR_KIN_V PROSITE (2)
           Transcript 1 (1) 1.---------------------Exon 1.4  PDB: A:51-203 UniProt: 43-271 [INCOMPLETE]                                                                                                      Transcript 1 (1)
           Transcript 1 (2) -Exon 1.3  PDB: A:29-50--------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2qbx A  28 EETLMDSTTATAELGWMVHPPSGWEEVSGYDENMNTIRTYQVCNVFESSQNNWLRTKFIRRRGAHRIHVEMKFSVRDCSSIPSVPGSCKETFNLYYYEADFDSATKTFPNWMENPWVKVDTIAADESFSQVDLGGRVMKINTEVRSFGPVSRSGFYLAFQDYGGCMSLIAVRVFYR 203
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197      

Chain B from PDB  Type:PROTEIN  Length:176
 aligned with EPHB2_HUMAN | P29323 from UniProtKB/Swiss-Prot  Length:1055

    Alignment length:176
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189      
          EPHB2_HUMAN    20 EETLMDSTTATAELGWMVHPPSGWEEVSGYDENMNTIRTYQVCNVFESSQNNWLRTKFIRRRGAHRIHVEMKFSVRDCSSIPSVPGSCKETFNLYYYEADFDSATKTFPNWMENPWVKVDTIAADESFSQVDLGGRVMKINTEVRSFGPVSRSGFYLAFQDYGGCMSLIAVRVFYR 195
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qbxB00 B:28-203 Galactose-binding domain-like                                                                                                                                   CATH domains
           Pfam domains (1) Ephrin_lbd-2qbxB01 B:28-203                                                                                                                                                      Pfam domains (1)
           Pfam domains (2) Ephrin_lbd-2qbxB02 B:28-203                                                                                                                                                      Pfam domains (2)
         Sec.struct. author .eeeee.hhh......eee.....eeeeee.....eeeeeeee........eeee...ee......eeeeeeeee.hhhhh.........eeeeeeeee.................eeeeeee.....eeee....eeeeeeeeeee......eeeeeeee...eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) EPH_LBD  PDB: B:28-203 UniProt: 20-202                                                                                                                                           PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------RECEPTOR_TYR_KIN_V PROSITE (2)
           Transcript 1 (1) 1.---------------------Exon 1.4  PDB: B:51-203 UniProt: 43-271 [INCOMPLETE]                                                                                                      Transcript 1 (1)
           Transcript 1 (2) -Exon 1.3  PDB: B:29-50--------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2qbx B  28 EETLMDSTTATAELGWMVHPPSGWEEVSGYDENMNTIRTYQVCNVFESSQNNWLRTKFIRRRGAHRIHVEMKFSVRDCSSIPSVPGSCKETFNLYYYEADFDSATKTFPNWMENPWVKVDTIAADESFSQVDLGGRVMKINTEVRSFGPVSRSGFYLAFQDYGGCMSLIAVRVFYR 203
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197      

Chain D from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 2qbx D   1 SNEWIQPRLPQ  11
                                    10 

Chain P from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 2qbx P   1 SNEWIQPRL   9

   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  (0, 0)

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

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: GBD (153)

(-) Gene Ontology  (54, 54)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (EPHB2_HUMAN | P29323)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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: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: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:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    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.
    GO:0005005    transmembrane-ephrin receptor activity    Combining with a transmembrane ephrin to initiate a change in cell activity.
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    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:0048593    camera-type eye morphogenesis    The process in which the anatomical structures of the eye are generated and organized. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
    GO:0000902    cell morphogenesis    The developmental process in which the size or shape of a cell is generated and organized.
    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:0071679    commissural neuron axon guidance    The process in which the migration of an axon growth cone of a commissural neuron is directed to its target in the brain in response to a combination of attractive and repulsive cues.
    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:0048013    ephrin receptor signaling pathway    The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
    GO:0042472    inner ear morphogenesis    The process in which the anatomical structures of the inner ear are generated and organized. The inner ear is the structure in vertebrates that contains the organs of balance and hearing. It consists of soft hollow sensory structures (the membranous labyrinth) containing fluid (endolymph) surrounded by fluid (perilymph) and encased in a bony cavity (the bony labyrinth). It consists of two chambers, the sacculus and utriculus, from which arise the cochlea and semicircular canals respectively.
    GO:0007612    learning    Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.
    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:0050771    negative regulation of axonogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of axonogenesis.
    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:0021631    optic nerve morphogenesis    The process in which the anatomical structure of the optic nerve is generated and organized. The sensory optic nerve originates from the bipolar cells of the retina and conducts visual information to the brainstem. The optic nerve exits the back of the eye in the orbit, enters the optic canal, and enters the central nervous system at the optic chiasm (crossing) where the nerve fibers become the optic tract just prior to entering the hindbrain.
    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:0048170    positive regulation of long-term neuronal synaptic plasticity    A process that increases long-term neuronal synaptic plasticity, the ability of neuronal synapses to change long-term as circumstances require. Long-term neuronal synaptic plasticity generally involves increase or decrease in actual synapse numbers.
    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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    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:0050878    regulation of body fluid levels    Any process that modulates the levels of body fluids.
    GO:0048168    regulation of neuronal synaptic plasticity    A process that modulates neuronal synaptic plasticity, the ability of neuronal synapses to change as circumstances require. They may alter function, such as increasing or decreasing their sensitivity, or they may increase or decrease in actual numbers.
    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: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:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    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:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:161 - Gly A:162   [ RasMol ]  
    Gly A:175 - Pro A:176   [ RasMol ]  
    Gly B:175 - Pro B:176   [ RasMol ]  
    His A:46 - Pro A:47   [ RasMol ]  
    His B:46 - Pro B:47   [ RasMol ]  
    Phe A:135 - Pro A:136   [ RasMol ]  
    Phe B:135 - Pro B:136   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2qbx
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  EPHB2_HUMAN | P29323
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.10.1
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  EPHB2_HUMAN | P29323
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        EPHB2_HUMAN | P293231b4f 1f0m 3zfm

(-) Related Entries Specified in the PDB File

1kgy EPHB2/EPHRINB2 COMPLEX STRUCTURE
1nuk APO LIGAND BINDING DOMAIN OF THE EPHB2 RECEPTOR
2bba EPHB4/ANTAGONISTIC TNYL-RAW COMPLEX STRUCTURE