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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DOMAIN V FROM BETA2-GLYCOPROTEIN I
 
Authors :  A. Kolyada, C. -J. Lee, A. De Biasio, N. Beglova
Date :  31 Aug 10  (Deposition) - 05 Jan 11  (Release) - 30 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Sushi, Antiphospholipid Syndrome, Anionic Phospholipids Binding, Lipoprotein Receptors Binding, Blood Plasma, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Kolyada, C. J. Lee, A. De Biasio, N. Beglova
A Novel Dimeric Inhibitor Targeting Beta2Gpi In Beta2Gpi/Antibody Complexes Implicated In Antiphospholipid Syndrome.
Plos One V. 5 E1534 2010
PubMed-ID: 21179511  |  Reference-DOI: 10.1371/JOURNAL.PONE.0015345

(-) Compounds

Molecule 1 - BETA-2-GLYCOPROTEIN 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    FragmentDOMAIN V (UNP RESIDUES 263-345)
    GeneAPOH, B2GPI
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBETA-2-GLYCOPROTEIN I, BETA(2)GPI, B2GPI, APOLIPOPROTEIN H, APO-H, ACTIVATED PROTEIN C-BINDING PROTEIN, APC INHIBITOR, ANTICARDIOLIPIN COFACTOR

 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, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:55 , LYS A:282 , LYS A:284 , LYS A:308BINDING SITE FOR RESIDUE SO4 A 3
2AC2SOFTWAREHOH A:10 , LYS A:251 , PRO A:304 , LYS A:305 , SER A:312BINDING SITE FOR RESIDUE SO4 A 2
3AC3SOFTWAREHOH B:29 , LYS B:251 , PRO B:304 , LYS B:305 , SER B:312BINDING SITE FOR RESIDUE SO4 B 1
4AC4SOFTWAREHOH B:106 , LYS B:282 , LYS B:317BINDING SITE FOR RESIDUE SO4 B 4

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:245 -A:296
2A:281 -A:306
3A:288 -A:326
4B:245 -B:296
5B:281 -B:306
6B:288 -B:326

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OP8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_000673V266LAPOH_HUMANPolymorphism4581A/BL247L
2UniProtVAR_008170C325GAPOH_HUMANPolymorphism1801689A/BC306G
3UniProtVAR_008171W335SAPOH_HUMANPolymorphism1801690A/BW316S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_000673V266LAPOH_HUMANPolymorphism4581AL247L
2UniProtVAR_008170C325GAPOH_HUMANPolymorphism1801689AC306G
3UniProtVAR_008171W335SAPOH_HUMANPolymorphism1801690AW316S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_000673V266LAPOH_HUMANPolymorphism4581BL247L
2UniProtVAR_008170C325GAPOH_HUMANPolymorphism1801689BC306G
3UniProtVAR_008171W335SAPOH_HUMANPolymorphism1801690BW316S

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OP8)

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002059481ENSE00001149177chr17:64225556-64225434123APOH_HUMAN1-22220--
1.2ENST000002059482ENSE00000742667chr17:64224314-64224138177APOH_HUMAN22-81600--
1.3ENST000002059483ENSE00000742665chr17:64222242-6422214697APOH_HUMAN81-113330--
1.4ENST000002059484ENSE00000742663chr17:64219892-6421981677APOH_HUMAN113-139270--
1.5ENST000002059485ENSE00000742652chr17:64216860-64216672189APOH_HUMAN139-202640--
1.6ENST000002059486ENSE00000584156chr17:64213085-64212906180APOH_HUMAN202-262612A:243-243
B:243-243
1
1
1.7ENST000002059487ENSE00000742648chr17:64210768-64210571198APOH_HUMAN262-328672A:243-309
B:243-309
67
67
1.8ENST000002059488ENSE00000837173chr17:64208306-64208148159APOH_HUMAN328-345182A:309-326
B:309-326
18
18

(-) 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:85
 aligned with APOH_HUMAN | P02749 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:85
                                                                                                             345 
                                   271       281       291       301       311       321       331       341   | 
           APOH_HUMAN   262 ASCKVPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEHSSLAFWKTDASDVKPC-   -
               SCOP domains d3op8a_ A: beta2-glycoprotein I                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee..eeeehhhhh........eeeeeeee....eeeeeeeeee..ee.................hhhhh.... Sec.struct. author
                 SAPs(SNPs) ----L----------------------------------------------------------G---------S----------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1-----------------------------------------------------------------Exon 1.8          - Transcript 1 (1)
           Transcript 1 (2) Exon 1.7  PDB: A:243-309 UniProt: 262-328                          ------------------ Transcript 1 (2)
                 3op8 A 243 GSCKLPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEHSSLAFWKTDASDVKPCA 327
                                   252       262       272       282       292       302       312       322     

Chain B from PDB  Type:PROTEIN  Length:85
 aligned with APOH_HUMAN | P02749 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:85
                                                                                                             345 
                                   271       281       291       301       311       321       331       341   | 
           APOH_HUMAN   262 ASCKVPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEHSSLAFWKTDASDVKPC-   -
               SCOP domains d3op8b_ B: beta2-glycoprotein I                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Sushi_2-3op8B01 B:244-326                                                          - Pfam domains (1)
           Pfam domains (2) -Sushi_2-3op8B02 B:244-326                                                          - Pfam domains (2)
         Sec.struct. author .ee.......eeee..eeeehhhhh...ee...eeeeeeee....eeeeeeeeee..ee.................hhhhh.... Sec.struct. author
                 SAPs(SNPs) ----L----------------------------------------------------------G---------S----------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1-----------------------------------------------------------------Exon 1.8          - Transcript 1 (1)
           Transcript 1 (2) Exon 1.7  PDB: B:243-309 UniProt: 262-328                          ------------------ Transcript 1 (2)
                 3op8 B 243 GSCKLPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEHSSLAFWKTDASDVKPCA 327
                                   252       262       272       282       292       302       312       322     

   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  (0, 0)

(no "CATH Domain" information available for 3OP8)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (39, 39)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (APOH_HUMAN | P02749)
molecular function
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0060230    lipoprotein lipase activator activity    Binds to and increases the activity of a lipoprotein lipase, an enzyme that catalyzes of the hydrolysis of a lipid within a lipoprotein.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
    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).
biological process
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0031100    animal organ regeneration    The regrowth of a lost or destroyed animal organ.
    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:0007597    blood coagulation, intrinsic pathway    A protein activation cascade that contributes to blood coagulation and consists of the interactions among high molecular weight kininogen, prekallikrein, and factor XII that lead to the activation of clotting factor X.
    GO:0016525    negative regulation of angiogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
    GO:0030195    negative regulation of blood coagulation    Any process that stops, prevents, or reduces the frequency, rate or extent of blood coagulation.
    GO:0010596    negative regulation of endothelial cell migration    Any process that decreases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
    GO:0001937    negative regulation of endothelial cell proliferation    Any process that stops, prevents, or reduces the rate or extent of endothelial cell proliferation.
    GO:0051918    negative regulation of fibrinolysis    Any process that stops, prevents, or reduces the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots.
    GO:0033033    negative regulation of myeloid cell apoptotic process    Any process that stops, prevents, or reduces the frequency, rate, or extent of a myeloid cell apoptotic process.
    GO:0060268    negative regulation of respiratory burst    Any process that decreases the rate frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals.
    GO:0034392    negative regulation of smooth muscle cell apoptotic process    Any process that stops, prevents, or reduces the frequency, rate, or extent of smooth muscle cell apoptotic process.
    GO:0031639    plasminogen activation    The process in which inactive plasminogen is processed to active plasmin. This process includes cleavage at an internal Arg-Val site to form an N-terminal A-chain and C-terminal B-chain held together by a disulfide bond, and can include further proteolytic cleavage events to remove the preactivation peptide.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    GO:0030194    positive regulation of blood coagulation    Any process that activates or increases the frequency, rate or extent of blood coagulation.
    GO:0051006    positive regulation of lipoprotein lipase activity    Any process that activates or increases the activity of the enzyme lipoprotein lipase.
    GO:0010898    positive regulation of triglyceride catabolic process    Any process that increases the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of triglyceride.
    GO:0030193    regulation of blood coagulation    Any process that modulates the frequency, rate or extent of blood coagulation.
    GO:0051917    regulation of fibrinolysis    Any process that modulates the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots.
    GO:0034014    response to triglyceride    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 triglyceride stimulus.
    GO:0006641    triglyceride metabolic process    The chemical reactions and pathways involving triglyceride, any triester of glycerol. The three fatty acid residues may all be the same or differ in any permutation. Triglycerides are important components of plant oils, animal fats and animal plasma lipoproteins.
    GO:0034197    triglyceride transport    The directed movement of triglyceride into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Triglycerides are important components of plant oils, animal fats and animal plasma lipoproteins.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0042627    chylomicron    A large lipoprotein particle (diameter 75-1200 nm) composed of a central core of triglycerides and cholesterol surrounded by a protein-phospholipid coating. The proteins include one molecule of apolipoprotein B-48 and may include a variety of apolipoproteins, including APOAs, APOCs and APOE. Chylomicrons are found in blood or lymph and carry lipids from the intestines into other body tissues.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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:0034364    high-density lipoprotein particle    A lipoprotein particle with a high density (typically 1.063-1.21 g/ml) and a diameter of 5-10 nm that contains APOAs and may contain APOCs and APOE; found in blood and carries lipids from body tissues to the liver as part of the reverse cholesterol transport process.
    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:0031089    platelet dense granule lumen    The volume enclosed by the membrane of the platelet dense granule.
    GO:0034361    very-low-density lipoprotein particle    A triglyceride-rich lipoprotein particle that is typically composed of APOB100, APOE and APOCs and has a density of about 1.006 g/ml and a diameter of between 20-80 nm. It is found in blood and transports endogenous products (newly synthesized cholesterol and triglycerides) from the liver.

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 Related Entries

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

UniProtKB/Swiss-Prot
        APOH_HUMAN | P027491c1z 1g4f 1g4g 1qub 2kri 4jhs

(-) Related Entries Specified in the PDB File

1c1z 1qub