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 :  CRYSTAL STRUCTURE OF LATENT HUMAN C1-INHIBITOR
 
Authors :  V. Harmat, L. Beinrohr, P. Gal, J. Dobo
Date :  18 Dec 06  (Deposition) - 01 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Latent Serpin; Rcl Insertion, Immune System, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Beinrohr, V. Harmat, J. Dobo, Z. Lorincz, P. Gal, P. Zavodszky
C1 Inhibitor Serpin Domain Structure Reveals The Likely Mechanism Of Heparin Potentiation And Conformational Diseas
J. Biol. Chem. V. 282 21100 2007
PubMed-ID: 17488724  |  Reference-DOI: 10.1074/JBC.M700841200

(-) Compounds

Molecule 1 - PLASMA PROTEASE C1 INHIBITOR
    ChainsA
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPPIC9K
    Expression System StrainGS115
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    FragmentSERPIN DOMAIN
    GeneSERPING1, C1IN, C1NH
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymC1-INHIBITOR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:216 , SER A:258 , ARG A:444BINDING SITE FOR RESIDUE NAG A 500
2AC2SOFTWAREHOH A:61 , HIS A:312 , PHE A:313 , ILE A:314 , LYS A:321 , LYS A:393 , GLU A:395 , PHE A:396BINDING SITE FOR RESIDUE GOL A 5001
3AC3SOFTWAREHOH A:5 , HOH A:68 , HOH A:70 , LYS A:251 , GLU A:426BINDING SITE FOR RESIDUE GOL A 5002
4AC4SOFTWAREARG A:211 , ASP A:212 , THR A:213 , GLU A:410BINDING SITE FOR RESIDUE GOL A 5003

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:101 -A:406
2A:108 -A:183

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OAY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (41, 41)

Asymmetric/Biological Unit (41, 41)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_027379C130YIC1_HUMANDisease (HAE)  ---AC108Y
02UniProtVAR_068833Y154CIC1_HUMANDisease (HAE)281875168AY132C
03UniProtVAR_068834S170FIC1_HUMANDisease (HAE)281875169AS148F
04UniProtVAR_068835G184RIC1_HUMANDisease (HAE)281875170AG162R
05UniProtVAR_068836L230PIC1_HUMANDisease (HAE)281875171AL208P
06UniProtVAR_068837I232KIC1_HUMANDisease (HAE)281875172AI210K
07UniProtVAR_071702W265RIC1_HUMANDisease (HAE)  ---AW243R
08UniProtVAR_071703I274VIC1_HUMANDisease (HAE)  ---AI252V
09UniProtVAR_068839W299RIC1_HUMANDisease (HAE)281875173AW277R
10UniProtVAR_011751T308SIC1_HUMANPolymorphism1803212AT286S
11UniProtVAR_027376G345RIC1_HUMANDisease (HAE)  ---AG323R
12UniProtVAR_027380T394PIC1_HUMANDisease (HAE)  ---AT372P
13UniProtVAR_027381D408VIC1_HUMANDisease (HAE)  ---AD386V
14UniProtVAR_007013G429RIC1_HUMANDisease (HAE)  ---AG407R
15UniProtVAR_068840L430QIC1_HUMANDisease (HAE)281875174AL408Q
16UniProtVAR_068841M441TIC1_HUMANDisease (HAE)281875175AM419T
17UniProtVAR_068842L447PIC1_HUMANDisease (HAE)281875176AL425P
18UniProtVAR_007014V454EIC1_HUMANDisease (HAE)121907949AV432E
19UniProtVAR_007015A456EIC1_HUMANDisease (HAE)  ---AA434E
20UniProtVAR_007016A458TIC1_HUMANDisease (HAE)121907947AA436T
21UniProtVAR_007017A458VIC1_HUMANDisease (HAE)  ---AA436V
22UniProtVAR_007018A465VIC1_HUMANDisease (HAE)121907950AA443V
23UniProtVAR_007019R466CIC1_HUMANDisease (HAE)28940870AR444C
24UniProtVAR_007020R466HIC1_HUMANDisease (HAE)121907948AR444H
25UniProtVAR_007021R466LIC1_HUMANDisease (HAE)121907948AR444L
26UniProtVAR_007022R466SIC1_HUMANDisease (HAE)28940870AR444S
27UniProtVAR_007023T467PIC1_HUMANDisease (HAE)  ---AT445P
28UniProtVAR_027382V473EIC1_HUMANDisease (HAE)  ---AV451E
29UniProtVAR_068843V473GIC1_HUMANDisease (HAE)281875177AV451G
30UniProtVAR_007024V473MIC1_HUMANDisease (HAE)  ---AV451M
31UniProtVAR_007025Q474EIC1_HUMANPolymorphism  ---AQ452E
32UniProtVAR_007026F477SIC1_HUMANDisease (HAE)  ---AF455S
33UniProtVAR_007027V480MIC1_HUMANPolymorphism4926AM458M
34UniProtVAR_007028L481PIC1_HUMANDisease (HAE)  ---AL459P
35UniProtVAR_007029L481RIC1_HUMANDisease (HAE)  ---AL459R
36UniProtVAR_007030P489RIC1_HUMANDisease (HAE)  ---AP467R
37UniProtVAR_027383G493EIC1_HUMANDisease (HAE)  ---AG471E
38UniProtVAR_071704G493RIC1_HUMANDisease (HAE)  ---AG471R
39UniProtVAR_068844D497GIC1_HUMANDisease (HAE)281875178AD475G
40UniProtVAR_027384P498RIC1_HUMANDisease (HAE)  ---AP476R
41UniProtVAR_007031P498SIC1_HUMANDisease (HAE)  ---AP476S

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SERPINPS00284 Serpins signature.IC1_HUMAN471-481  1A:449-459

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002784071bENSE00001941568chr11:57364991-57365195205IC1_HUMAN-00--
1.2eENST000002784072eENSE00002142743chr11:57365722-5736579473IC1_HUMAN1-17170--
1.3dENST000002784073dENSE00001371628chr11:57367352-57367850499IC1_HUMAN18-1841671A:101-162 (gaps)62
1.4aENST000002784074aENSE00000988934chr11:57369508-57369642135IC1_HUMAN184-229461A:162-20746
1.5bENST000002784075bENSE00000988935chr11:57373483-57373686204IC1_HUMAN229-297691A:207-27569
1.6cENST000002784076cENSE00000988936chr11:57373881-57374020140IC1_HUMAN297-343471A:275-321 (gaps)47
1.8bENST000002784078bENSE00000988937chr11:57379190-57379409220IC1_HUMAN344-417741A:322-39574
1.9iENST000002784079iENSE00001769777chr11:57381801-57382326526IC1_HUMAN417-500841A:395-47682

(-) 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:368
 aligned with IC1_HUMAN | P05155 from UniProtKB/Swiss-Prot  Length:500

    Alignment length:376
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492      
            IC1_HUMAN   123 CPGPVTLCSDLESHSTEAVLGDALVDFSLKLYHAFSAMKKVETNMAFSPFSIASLLTQVLLGAGENTKTNLESILSYPKDFTCVHQALKGFTTKGVTSVSQIFHSPDLAIRDTFVNASRTLYSSSPRVLSNNSDANLELINTWVAKNTNNKISRLLDSLPSDTRLVLLNAIYLSAKWKTTFDPKKTRMEPFHFKNSVIKVPMMNSKKYPVAHFIDQTLKAKVGQLQLSHNLSLVILVPQNLKHRLEDMEQALSPSVFKAIMEKLEMSKFQPTLLTLPRIKVTTSQDMLSIMEKLEFFDFSYDLNLCGLTEDPDLQVSAMQHQTVLELTETGVEAAAASAISVARTLLVFEVQQPFLFVLWDQQHKFPVFMGRVYDP 498
               SCOP domains --  d2oaya1 A:105-476 automated match    es                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --  -----------------Serpin-2oayA01 A    :122-476                                                                                                                                                                                                                                                                                                                                        Pfam domains
         Sec.struct. author ..--.......hhhhhhhhhhhhhhhhhhhhhhhhh.----...eeehhhhhhhhhhhhhhh.hhhhhhhhhhhhh......hhhhhhhh.....eeeeeeeee......hhhhhhhhhhhhh...ee...hhhhhhhhhhhhhhhh.................eeeeeeeeeeee..........eeeee..--..eeeeeeeeeeeeeeeeee....eeeeeee....eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeehhhhhhhhh..hhhhhh...............eeeeeeeee...eeeeeeeeee.....eee......eeeeeee....eeeeeeee... Sec.struct. author
             SAPs(SNPs) (1) -------Y-----------------------C---------------F-------------R---------------------------------------------P-K--------------------------------R--------V------------------------R--------S------------------------------------R------------------------------------------------P-------------V--------------------RQ----------T-----P------E-E-T------VCP-----EE--S--MP-------R---E---GR SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V-------H------G-------R-----------R----S SAPs(SNPs) (2)
             SAPs(SNPs) (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L------M------------------------- SAPs(SNPs) (3)
             SAPs(SNPs) (4) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S-------------------------------- SAPs(SNPs) (4)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     ----------------- PROSITE
           Transcript 1 (1) Exon 1.3d  PDB: A:101-162 (gaps) UniProt: 18-184 [INCOMPLETE] --------------------------------------------Exon 1.5b  PDB: A:207-275 UniProt: 229-297                           ----------------------------------------------Exon 1.8b  PDB: A:322-395 UniProt: 344-417                                --------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------Exon 1.4a  PDB: A:162-207 UniProt: 184-229    -------------------------------------------------------------------Exon 1.6c  PDB: A:275-321 (gaps)               -------------------------------------------------------------------------Exon 1.9i  PDB: A:395-476 UniProt: 417-500 [INCOMPLETE]                            Transcript 1 (2)
                 2oay A 101 CP--VTLCSDLESHSTEAVLGDALVDFSLKLYHAFSA----ETNMAFSPFSIASLLTQVLLGAGENTKTNLESILSYPKDFTCVHQALKGFTTKGVTSVSQIFHSPDLAIRDTFVNASRTLYSSSPRVLSNNSDANLELINTWVAKNTNNKISRLLDSLPSDTRLVLLNAIYLSAKWKTTFDPKKTRMEPFHF--SVIKVPMMNSKKYPVAHFIDQTLKAKVGQLQLSHNLSLVILVPQNLKHRLEDMEQALSPSVFKAIMEKLEMSKFQPTLLTLPRIKVTTSQDMLSIMEKLEFFDFSYDLNLCGLTEDPDLQVSAMQHQTVLELTETGVEAAAASAISVARTLLVFEVQQPFLFMLWDQQHKFPVFMGRVYDP 476
                             |  |  110       120       130      |  - |     150       160       170       180       190       200       210       220       230       240       250       260       270       280       290  |  | 300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470      
                             |  |                             137  142                                                                                                                                                    293  |                                                                                                                                                                                    
                           102  |                                                                                                                                                                                            296                                                                                                                                                                                    
                              105                                                                                                                                                                                                                                                                                                                                                                                   

   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  (0, 0)

(no "CATH Domain" information available for 2OAY)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IC1_HUMAN | P05155)
molecular function
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    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:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
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:0008015    blood circulation    The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
    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:0006958    complement activation, classical pathway    Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
    GO:0042730    fibrinolysis    A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0001869    negative regulation of complement activation, lectin pathway    Any process that stops, prevents, or reduces the rate of complement activation by the lectin pathway.
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
cellular component
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    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: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:0031093    platelet alpha granule lumen    The volume enclosed by the membrane of the platelet alpha granule.

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2oay)
 

(-) 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
  2oay
    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
  IC1_HUMAN | P05155
    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)
  106100
    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
  IC1_HUMAN | P05155
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        IC1_HUMAN | P051551m6q 5du3 5duq

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2OAY)