Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF THE METAL-FREE GAMMA-CARBOXYGLUTAMIC ACID-RICH MEMBRANE BINDING REGION OF FACTOR IX BY TWO-DIMENSIONAL NMR SPECTROSCOPY
 
Authors :  S. J. Freedman, B. C. Furie, B. Furie, J. D. Baleja
Date :  26 Feb 95  (Deposition) - 10 Jul 95  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (15x)
Keywords :  Coagulation Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. J. Freedman, B. C. Furie, B. Furie, J. D. Baleja
Structure Of The Metal-Free Gamma-Carboxyglutamic Acid-Rich Membrane Binding Region Of Factor Ix By Two-Dimensional Nmr Spectroscopy.
J. Biol. Chem. V. 270 7980 1995
PubMed-ID: 7713897  |  Reference-DOI: 10.1074/JBC.270.14.7980
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COAGULATION FACTOR IX
    ChainsA
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  
NMR Structure (15x)

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 12)
No.NameCountTypeFull Name
1FMT12Ligand/IonFORMIC ACID

(-) Sites  (12, 12)

NMR Structure (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:7 , GLU A:8BINDING SITE FOR RESIDUE FMT A 48
02AC2SOFTWARETYR A:1 , GLU A:8BINDING SITE FOR RESIDUE FMT A 49
03AC3SOFTWAREGLU A:15BINDING SITE FOR RESIDUE FMT A 50
04AC4SOFTWAREGLU A:17 , LYS A:22BINDING SITE FOR RESIDUE FMT A 51
05AC5SOFTWAREGLU A:20BINDING SITE FOR RESIDUE FMT A 52
06AC6SOFTWAREGLU A:21 , SER A:24BINDING SITE FOR RESIDUE FMT A 53
07AC7SOFTWAREGLU A:26BINDING SITE FOR RESIDUE FMT A 54
08AC8SOFTWAREGLU A:27BINDING SITE FOR RESIDUE FMT A 55
09AC9SOFTWAREGLU A:30 , VAL A:31 , PHE A:32BINDING SITE FOR RESIDUE FMT A 56
10BC1SOFTWAREPHE A:32 , GLU A:33BINDING SITE FOR RESIDUE FMT A 57
11BC2SOFTWAREGLU A:36BINDING SITE FOR RESIDUE FMT A 58
12BC3SOFTWAREGLU A:40BINDING SITE FOR RESIDUE FMT A 59

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:18 -A:23

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (20, 20)

NMR Structure (20, 20)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_006530N48IFA9_HUMANDisease (HEMB)  ---AN2I
02UniProtVAR_006531S49PFA9_HUMANDisease (HEMB)  ---AS3P
03UniProtVAR_017344L52SFA9_HUMANDisease (HEMB)  ---AL6S
04UniProtVAR_006532E53AFA9_HUMANDisease (HEMB)  ---AE7A
05UniProtVAR_073976E54DFA9_HUMANUnclassified (HEMB)  ---AE8D
06UniProtVAR_006533E54GFA9_HUMANDisease (HEMB)  ---AE8G
07UniProtVAR_006534F55CFA9_HUMANDisease (HEMB)  ---AF9C
08UniProtVAR_006535G58AFA9_HUMANDisease (HEMB)  ---AG12A
09UniProtVAR_073977G58EFA9_HUMANUnclassified (HEMB)  ---AG12E
10UniProtVAR_006536G58RFA9_HUMANDisease (HEMB)  ---AG12R
11UniProtVAR_006538E66VFA9_HUMANDisease (HEMB)  ---AE20V
12UniProtVAR_006539E67KFA9_HUMANDisease (HEMB)  ---AE21K
13UniProtVAR_006540F71SFA9_HUMANDisease (HEMB)  ---AF25S
14UniProtVAR_006541E73KFA9_HUMANDisease (HEMB)137852225AE27K
15UniProtVAR_006542E73VFA9_HUMANDisease (HEMB)137852226AE27V
16UniProtVAR_017308R75QFA9_HUMANDisease (HEMB)137852228AR29Q
17UniProtVAR_017309E79DFA9_HUMANDisease (HEMB)137852229AE33D
18UniProtVAR_017345T84RFA9_HUMANDisease (HEMB)  ---AT38R
19UniProtVAR_006543Y91CFA9_HUMANDisease (HEMB)  ---AY45C
20UniProtVAR_006544D93GFA9_HUMANDisease (HEMB)137852230AD47G

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

(-) PROSITE Motifs  (4, 3)

NMR Structure (4, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLA_2PS50998 Gla domain profile.FA9_HUMAN47-93  1A:1-47
2GLA_1PS00011 Vitamin K-dependent carboxylation domain.FA9_HUMAN63-88  1A:17-42
3EGF_3PS50026 EGF-like domain profile.FA9_HUMAN93-129  1A:47-47
4EGF_CAPS01187 Calcium-binding EGF-like domain signature.FA9_HUMAN93-117  1A:47-47

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002180991bENSE00002195519X:138612917-13861301195FA9_HUMAN1-30300--
1.2bENST000002180992bENSE00000677287X:138619169-138619332164FA9_HUMAN30-84551A:1-3838
1.3ENST000002180993ENSE00001173335X:138619521-13861954525FA9_HUMAN85-9391A:39-479
1.4aENST000002180994aENSE00001173327X:138623235-138623348114FA9_HUMAN93-131391A:47-471
1.5bENST000002180995bENSE00001173320X:138630522-138630650129FA9_HUMAN131-174440--
1.6ENST000002180996ENSE00001173315X:138633221-138633423203FA9_HUMAN174-241680--
1.7ENST000002180997ENSE00001173311X:138642900-138643014115FA9_HUMAN242-280390--
1.8bENST000002180998bENSE00001029145X:138643683-1386456171935FA9_HUMAN280-4611820--

(-) Sequences/Alignments

NMR Structure
   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:47
 aligned with FA9_HUMAN | P00740 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:47
                                    56        66        76        86       
             FA9_HUMAN   47 YNSGKLEEFVQGNLERECMEEKCSFEEAREVFENTERTTEFWKQYVD 93
               SCOP domains d1cfha_ A: Coagulation factor IX (IXa)          SCOP domains
               CATH domains 1cfhA00 A:1-47 Coagulation Factor IX            CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author ....................................hhhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) -IP--SADC--A-------VK---S-K-Q---D----R------C-G SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------G---E--------------V-------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) -----------R----------------------------------- SAPs(SNPs) (3)
                PROSITE (1) GLA_2  PDB: A:1-47 UniProt: 47-93               PROSITE (1)
                PROSITE (2) ----------------GLA_1  PDB: A:17-42       ----E PROSITE (2)
                PROSITE (3) ----------------------------------------------E PROSITE (3)
           Transcript 1 (1) Exon 1.2b  PDB: A:1-38 UniProt: 30-84 Exon 1.3  Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------1 Transcript 1 (2)
                  1cfh A  1 YNSGKLEEFVQGNLERECMEEKCSFEEAREVFENTERTTEFWKQYVD 47
                                    10        20        30        40       

   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)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

NMR Structure(hide GO term definitions)
Chain A   (FA9_HUMAN | P00740)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    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:0007598    blood coagulation, extrinsic pathway    A protein activation cascade that contributes to blood coagulation and consists of the self-limited process linking exposure and activation of tissue factor to the activation of clotting factor X.
    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:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0017187    peptidyl-glutamic acid carboxylation    The gamma-carboxylation of peptidyl-glutamic acid; catalyzed by the vitamin K dependent gamma-glutamyl carboxylase.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006465    signal peptide processing    The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell.
    GO:0031638    zymogen activation    The proteolytic processing of an inactive enzyme to an active form.
cellular component
    GO:0005796    Golgi lumen    The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    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: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

NMR Structure
  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
    FMT  [ 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
(no "Cis Peptide Bonds" information available for 1cfh)
 

(-) 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
  1cfh
    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
  FA9_HUMAN | P00740
    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)
  306900
    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
  FA9_HUMAN | P00740
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        FA9_HUMAN | P007401cfi 1edm 1ixa 1mgx 1nl0 1rfn 2wph 2wpi 2wpj 2wpk 2wpl 2wpm 3kcg 3lc3 3lc5 4wm0 4wma 4wmb 4wmi 4wmk 4wn2 4wnh 4yzu 4z0k 4zae 5egm 5f84 5f85 5f86 5jb8 5jb9 5jba 5jbb 5jbc 5tno 5tnt

(-) Related Entries Specified in the PDB File

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