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(-) Description

Title :  ANGIOPOIETIN-2 RECEPTOR BINDING DOMAIN
 
Authors :  W. A. Barton, D. Tzvetkova, D. B. Nikolov
Date :  14 Mar 05  (Deposition) - 12 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Angiogenesis, Tie2 Binding, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. A. Barton, D. Tzvetkova, D. B. Nikolov
Structure Of The Angiopoietin-2 Receptor Binding Domain And Identification Of Surfaces Involved In Tie2 Recognition.
Structure V. 13 825 2005
PubMed-ID: 15893672  |  Reference-DOI: 10.1016/J.STR.2005.03.009
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANGIOPOIETIN-2
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRECEPTOR BINDING DOMAIN (RESIDUES 281-496)
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymANG-2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:429 , ASP A:431 , CYS A:433 , CYS A:435BINDING SITE FOR RESIDUE CA A 497
2AC2SOFTWAREASP B:429 , ASP B:431 , CYS B:433 , CYS B:435BINDING SITE FOR RESIDUE CA B 497

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:284 -A:313
2A:433 -A:435
3A:437 -A:450
4B:284 -B:313
5B:433 -B:435
6B:437 -B:450

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Z3S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049069V333IANGP2_HUMANPolymorphism7813215A/BV333I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049069V333IANGP2_HUMANPolymorphism7813215AV333I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049069V333IANGP2_HUMANPolymorphism7813215BV333I

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIBRINOGEN_C_1PS00514 Fibrinogen C-terminal domain signature.ANGP2_HUMAN445-457
 
  2A:445-457
B:445-457
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIBRINOGEN_C_1PS00514 Fibrinogen C-terminal domain signature.ANGP2_HUMAN445-457
 
  1A:445-457
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIBRINOGEN_C_1PS00514 Fibrinogen C-terminal domain signature.ANGP2_HUMAN445-457
 
  1-
B:445-457

(-) Exons   (5, 10)

Asymmetric Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003252031aENSE00001949798chr8:6420930-6420168763ANGP2_HUMAN1-96960--
1.2ENST000003252032ENSE00000924724chr8:6390008-6389853156ANGP2_HUMAN97-148520--
1.3ENST000003252033ENSE00000924725chr8:6385197-6385076122ANGP2_HUMAN149-189410--
1.4ENST000003252034ENSE00000924726chr8:6378931-6378699233ANGP2_HUMAN189-267790--
1.5aENST000003252035aENSE00001121511chr8:6377515-6377385131ANGP2_HUMAN267-310442A:280-310
B:280-310
31
31
1.6ENST000003252036ENSE00000979541chr8:6372299-6372198102ANGP2_HUMAN311-344342A:311-344
B:311-344
34
34
1.7ENST000003252037ENSE00001121499chr8:6371365-6371199167ANGP2_HUMAN345-400562A:345-400
B:345-400
56
56
1.8aENST000003252038aENSE00000979543chr8:6366583-6366453131ANGP2_HUMAN400-444452A:400-444
B:400-444
45
45
1.9cENST000003252039cENSE00001854410chr8:6360782-63571723611ANGP2_HUMAN444-496532A:444-495
B:444-495
52
52

(-) 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:216
 aligned with ANGP2_HUMAN | O15123 from UniProtKB/Swiss-Prot  Length:496

    Alignment length:216
                                   289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489      
          ANGP2_HUMAN   280 SFRDCAEVFKSGHTTNGIYTLTFPNSTEEIKAYCDMEAGGGGWTIIQRREDGSVDFQRTWKEYKVGFGNPSGEYWLGNEFVSQLTNQQRYVLKIHLKDWEGNEAYSLYEHFYLSSEELNYRIHLKGLTGTAGKISSISQPGNDFSTKDGDNDKCICKCSQMLTGGWWFDACGPSNLNGMYYPQRQNTNKFNGIKWYYWKGSGYSLKATTMMIRPAD 495
               SCOP domains d1z3sa_ A: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains 1z3sA01 A:280-410,A:486-495 Gamma Fibrinogen, chain A, domain 1                                                                    1z3sA02 A:411-485 Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2    1z3sA01    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhh......eeeeee......eeeeeee.......eeeeeee.........hhhhhhhh..........hhhhhhhhhhhh.eeeeeeee.....eeeeeeeeeee.hhhhh..eeeeeeee...........................hhhhhhh..........ee..................eehhhhh......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------I------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------FIBRINOGEN_C_-------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5a  PDB: A:280-310      Exon 1.6  PDB: A:311-344          Exon 1.7  PDB: A:345-400 UniProt: 345-400               -------------------------------------------Exon 1.9c  PDB: A:444-495 UniProt: 444-496           Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------Exon 1.8a  PDB: A:400-444 UniProt: 400-444   --------------------------------------------------- Transcript 1 (2)
                 1z3s A 280 EFRDCAEVFKSGHTTNGIYTLTFPNSTEEIKAYCDMEAGGGGWTIIQRREDGSVDFQRTWKEYKVGFGNPSGEYWLGNEFVSQLTNQQRYVLKIHLKDWEGNEAYSLYEHFYLSSEELNYRIHLKGLTGTAGKISSISQPGNDFSTKDGDNDKCICKCSQMLTGGWWFDACGPSNLNGMYYPQRQNTNKFNGIKWYYWKGSGYSLKATTMMIRPAD 495
                                   289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489      

Chain B from PDB  Type:PROTEIN  Length:216
 aligned with ANGP2_HUMAN | O15123 from UniProtKB/Swiss-Prot  Length:496

    Alignment length:216
                                   289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489      
          ANGP2_HUMAN   280 SFRDCAEVFKSGHTTNGIYTLTFPNSTEEIKAYCDMEAGGGGWTIIQRREDGSVDFQRTWKEYKVGFGNPSGEYWLGNEFVSQLTNQQRYVLKIHLKDWEGNEAYSLYEHFYLSSEELNYRIHLKGLTGTAGKISSISQPGNDFSTKDGDNDKCICKCSQMLTGGWWFDACGPSNLNGMYYPQRQNTNKFNGIKWYYWKGSGYSLKATTMMIRPAD 495
               SCOP domains d1z3sb_ B: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains 1z3sB01 B:280-410,B:486-495 Gamma Fibrinogen, chain A, domain 1                                                                    1z3sB02 B:411-485 Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2    1z3sB01    CATH domains
           Pfam domains (1) -Fibrinogen_C-1z3sB01 B:281-494                                                                                                                                                                                        - Pfam domains (1)
           Pfam domains (2) -Fibrinogen_C-1z3sB02 B:281-494                                                                                                                                                                                        - Pfam domains (2)
         Sec.struct. author ...hhhhhhh......eeeeee......eeeeeee.......eeeeeee.........hhhhhhhh..........hhhhhhhhhhhh.eeeeeeee.....eeeeeeeeeee.hhhhh..eeeeeeee...........................hhhhhhh..........ee..................eehhhhh......eeeeeee... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------I------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------FIBRINOGEN_C_-------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5a  PDB: B:280-310      Exon 1.6  PDB: B:311-344          Exon 1.7  PDB: B:345-400 UniProt: 345-400               -------------------------------------------Exon 1.9c  PDB: B:444-495 UniProt: 444-496           Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------Exon 1.8a  PDB: B:400-444 UniProt: 400-444   --------------------------------------------------- Transcript 1 (2)
                 1z3s B 280 EFRDCAEVFKSGHTTNGIYTLTFPNSTEEIKAYCDMEAGGGGWTIIQRREDGSVDFQRTWKEYKVGFGNPSGEYWLGNEFVSQLTNQQRYVLKIHLKDWEGNEAYSLYEHFYLSSEELNYRIHLKGLTGTAGKISSISQPGNDFSTKDGDNDKCICKCSQMLTGGWWFDACGPSNLNGMYYPQRQNTNKFNGIKWYYWKGSGYSLKATTMMIRPAD 495
                                   289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489      

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (32, 32)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ANGP2_HUMAN | O15123)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0030971    receptor tyrosine kinase binding    Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase activity.
biological process
    GO:0048014    Tie signaling pathway    The series of molecular signals generated as a consequence of a Tie protein (a receptor) binding to one of its physiological ligands (an angiopoietin).
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0031100    animal organ regeneration    The regrowth of a lost or destroyed animal organ.
    GO:0048514    blood vessel morphogenesis    The process in which the anatomical structures of blood vessels are generated and organized. The blood vessel is the vasculature carrying blood.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0071363    cellular response to growth factor stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus.
    GO:0007281    germ cell development    The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism.
    GO:0072012    glomerulus vasculature development    The biological process whose specific outcome is the progression of a glomerulus vasculature from an initial condition to its mature state. This process begins with the formation of the glomerulus vasculature and ends with the mature structure. The glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the glomerulus.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0060135    maternal process involved in female pregnancy    A reproductive process occurring in the mother that allows an embryo or fetus to develop within it.
    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:0016525    negative regulation of angiogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
    GO:0043537    negative regulation of blood vessel endothelial cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of the migration of the endothelial cells of blood vessels.
    GO:0010812    negative regulation of cell-substrate adhesion    Any process that decreases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules.
    GO:0050928    negative regulation of positive chemotaxis    Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a motile cell or organism towards a higher concentration in a concentration gradient of a specific chemical.
    GO:0045766    positive regulation of angiogenesis    Any process that activates or increases angiogenesis.
    GO:0014823    response to activity    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an activity stimulus.
    GO:0009749    response to glucose    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
    GO:0001666    response to hypoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0009612    response to mechanical stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
    GO:0014070    response to organic cyclic compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0009314    response to radiation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        ANGP2_HUMAN | O151231z3u 2gy7 4jzc 4zfg

(-) Related Entries Specified in the PDB File

1z3u