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

(-) Description

Title :  RECOMBINANT RAT ANNEXIN V, T72A MUTANT
 
Authors :  Y. D. Mo, M. A. Swairjo, C. W. Li, J. F. Head, B. A. Seaton
Date :  04 May 98  (Deposition) - 25 Nov 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Calcium Binding Protein, Phospholipid Membrane Binding Protein, Calcium-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Campos, Y. D. Mo, T. R. Mealy, C. W. Li, M. A. Swairjo, C. Balch, J. F. Head, G. Retzinger, J. R. Dedman, B. A. Seaton
Mutational And Crystallographic Analyses Of Interfacial Residues In Annexin V Suggest Direct Interactions With Phospholipid Membrane Components.
Biochemistry V. 37 8004 1998
PubMed-ID: 9609693  |  Reference-DOI: 10.1021/BI973142N
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANNEXIN V
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPKK233-2
    Expression System StrainJM101
    Expression System Taxid562
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymPLACENTAL ANTICOAGULANT PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1CA5Ligand/IonCALCIUM ION
2SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:26 , GLY A:28 , GLY A:30 , GLU A:70BINDING SITE FOR RESIDUE CA A 401
2AC2SOFTWARELYS A:68 , LEU A:71 , GLU A:76 , HOH A:636BINDING SITE FOR RESIDUE CA A 402
3AC3SOFTWAREGLY A:181 , LYS A:184 , GLY A:186 , GLU A:226 , HOH A:510 , HOH A:532BINDING SITE FOR RESIDUE CA A 407
4AC4SOFTWAREASP A:224 , THR A:227 , GLU A:232BINDING SITE FOR RESIDUE CA A 408
5AC5SOFTWAREMET A:257 , GLY A:259 , ALA A:260 , GLY A:261 , ASP A:301BINDING SITE FOR RESIDUE CA A 410
6AC6SOFTWAREARG A:23 , LYS A:27 , GLY A:28 , ARG A:61 , HOH A:634BINDING SITE FOR RESIDUE SO4 A 450

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BCW)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ANNEXINPS00223 Annexins repeated domain signature.ANXA5_RAT30-82
102-154
186-238
261-313
  4A:30-82
A:102-154
A:186-238
A:261-313

(-) Exons   (0, 0)

(no "Exon" information available for 1BCW)

(-) Sequences/Alignments

Asymmetric/Biological 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:318
 aligned with ANXA5_RAT | P14668 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:318
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311        
            ANXA5_RAT     2 ALRGTVTDFSGFDGRADAEVLRKAMKGLGTDEDSILNLLTARSNAQRQQIAEEFKTLFGRDLVNDMKSELTGKFEKLIVALMKPSRLYDAYELKHALKGAGTDEKVLTEIIASRTPEELRAIKQAYEEEYGSNLEDDVVGDTSGYYQRMLVVLLQANRDPDTAIDDAQVELDAQALFQAGELKWGTDEEKFITILGTRSVSHLRRVFDKYMTISGFQIEETIDRETSGNLENLLLAVVKSIRSIPAYLAETLYYAMKGAGTDDHTLIRVIVSRSEIDLFNIRKEFRKNFATSLYSMIKGDTSGDYKKALLLLCGGEDD 319
               SCOP domains d1bcwa_ A: Annexin V                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ----------1bcwA01 A:12-84  [code=1.10.220.10, no name defined]                     1bcwA02 A:85-158  [code=1.10.220.10, no name defined]                     1bcwA03 A:159-244  [code=1.10.220.10, no name defined]                                1bcwA04 A:245-316  [code=1.10.220.10, no name defined]                  --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhhhhhhh........hhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhh...........hhhhhhhhhhhhhh........hhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhh......hhhhhhhhhhh....hhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------ANNEXIN  PDB: A:30-82 UniProt: 30-82                 -------------------ANNEXIN  PDB: A:102-154 UniProt: 102-154             -------------------------------ANNEXIN  PDB: A:186-238 UniProt: 186-238             ----------------------ANNEXIN  PDB: A:261-313 UniProt: 261-313             ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1bcw A   2 ALRGTVTDFSGFDGRADAEVLRKAMKGLGTDEDSILNLLTARSNAQRQQIAEEFKTLFGRDLVNDMKSELAGKFEKLIVALMKPSRLYDAYELKHALKGAGTDEKVLTEIIASRTPEELRAIKQAYEEEYGSNLEDDVVGDTSGYYQRMLVVLLQANRDPDTAIDDAQVELDAQALFQAGELKWGTDEEKFITILGTRSVSHLRRVFDKYMTISGFQIEETIDRETSGNLENLLLAVVKSIRSIPAYLAETLYYAMKGAGTDDHTLIRVIVSRSEIDLFNIRKEFRKNFATSLYSMIKGDTSGDYKKALLLLCGGEDD 319
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311        

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ANXA5_RAT | P14668)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0005544    calcium-dependent phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester, in the presence of calcium.
    GO:0005388    calcium-transporting ATPase activity    Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + Ca2+(cis) = ADP + phosphate + Ca2+(trans).
    GO:0017046    peptide hormone binding    Interacting selectively and non-covalently with any peptide with hormonal activity in animals.
    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:0030971    receptor tyrosine kinase binding    Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase activity.
biological process
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0070588    calcium ion transmembrane transport    A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0097211    cellular response to gonadotropin-releasing hormone    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 gonadotropin-releasing hormone stimulus. Gonadotropin-releasing hormone (GnRH) is a peptide hormone responsible for the release of follicle-stimulating hormone (FSH) and luteinizing hormone (LH) from the anterior pituitary. GnRH is synthesized and released by the hypothalamus.
    GO:0071284    cellular response to lead ion    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 lead ion stimulus.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0030195    negative regulation of blood coagulation    Any process that stops, prevents, or reduces the frequency, rate or extent of blood coagulation.
    GO:0050819    negative regulation of coagulation    Any process that stops, prevents, or reduces the frequency, rate or extent of coagulation.
    GO:1902721    negative regulation of prolactin secretion    Any process that stops, prevents or reduces the frequency, rate or extent of prolactin secretion.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:1901317    regulation of flagellated sperm motility    Any process that modulates the frequency, rate or extent of flagellated sperm motility.
    GO:0051592    response to calcium ion    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 calcium ion stimulus.
    GO:0097066    response to thyroid hormone    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 thyroid hormone stimulus.
cellular component
    GO:0030018    Z disc    Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
    GO:0043679    axon terminus    Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal button is a specialized region of it.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    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: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:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    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:0014704    intercalated disc    A complex cell-cell junction at which myofibrils terminate in cardiomyocytes; mediates mechanical and electrochemical integration between individual cardiomyocytes. The intercalated disc contains regions of tight mechanical attachment (fasciae adherentes and desmosomes) and electrical coupling (gap junctions) between adjacent cells.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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:0043204    perikaryon    The portion of the cell soma (neuronal cell body) that excludes the nucleus.
    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.
    GO:0042383    sarcolemma    The outer membrane of a muscle cell, consisting of the plasma membrane, a covering basement membrane (about 100 nm thick and sometimes common to more than one fiber), and the associated loose network of collagen fibers.
    GO:0008021    synaptic vesicle    A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1bcw)
 

(-) 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
  1bcw
    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
  ANXA5_RAT | P14668
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  ANXA5_RAT | P14668
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ANXA5_RAT | P146681a8a 1a8b 1bc0 1bc1 1bc3 1bcy 1bcz 1g5n 1n41 1n42 1n44 2h0k 2h0l 2h0m 2ie6 2ie7 2ran

(-) Related Entries Specified in the PDB File

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