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(-) Description

Title :  EPIDERMAL GROWTH FACTOR-LIKE DOMAIN FROM HUMAN FACTOR IX
 
Authors :  Z. Rao, P. Handford, M. Mayhew, V. Knott, G. G. Brownlee, D. Stuart
Date :  21 Mar 96  (Deposition) - 14 Oct 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  B,C
Keywords :  Crystal Structure, Epidermal Growth Factor, Egf, Calcium- Binding, Egf-Like Domain, Structure And Function, Human Factor Ix, Coagulation Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Rao, P. Handford, M. Mayhew, V. Knott, G. G. Brownlee, D. Stuart
The Structure Of A Ca(2+)-Binding Epidermal Growth Factor-Like Domain: Its Role In Protein-Protein Interactions.
Cell(Cambridge, Mass. ) V. 82 131 1995
PubMed-ID: 7606779  |  Reference-DOI: 10.1016/0092-8674(95)90059-4
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FACTOR IX
    ChainsB, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System GeneHUMAN FACTOR IX
    Expression System PlasmidPMA91
    Expression System Taxid562
    FragmentEPIDERMAL GROWTH FACTOR-LIKE DOMAIN
    GeneHUMAN FACTOR IX
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    StrainRZ1032, XL1-BLUE, MC1061

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:53 , HOH B:204 , HOH B:208 , HOH B:209 , HOH B:210 , HOH B:234 , HOH B:254BINDING SITE FOR RESIDUE CA B 3
2AC2SOFTWAREASN B:58 , ASP C:47 , GLY C:48 , GLN C:50 , ASP C:64 , ASP C:65BINDING SITE FOR RESIDUE CA C 1
3AC3SOFTWAREASP B:47 , GLY B:48 , GLN B:50 , ASP B:64 , ASP B:65 , ASN C:58BINDING SITE FOR RESIDUE CA B 2

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1B:51 -B:62
2B:56 -B:71
3B:73 -B:82
4C:51 -C:62
5C:56 -C:71
6C:73 -C:82

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (18, 36)

Asymmetric/Biological Unit (18, 36)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_006544D93GFA9_HUMANDisease (HEMB)137852230B/CD47G
02UniProtVAR_006545Q96PFA9_HUMANDisease (HEMB)137852231B/CQ50P
03UniProtVAR_006546C97SFA9_HUMANDisease (HEMB)  ---B/CC51S
04UniProtVAR_006547P101RFA9_HUMANDisease (HEMB)  ---B/CP55R
05UniProtVAR_006548C102RFA9_HUMANDisease (HEMB)  ---B/CC56R
06UniProtVAR_017346G106DFA9_HUMANDisease (HEMB)  ---B/CG60D
07UniProtVAR_006549G106SFA9_HUMANDisease (HEMB)137852233B/CG60S
08UniProtVAR_006550C108SFA9_HUMANDisease (HEMB)  ---B/CC62S
09UniProtVAR_006551D110NFA9_HUMANDisease (HEMB)137852274B/CD64N
10UniProtVAR_006552I112SFA9_HUMANDisease (HEMB)  ---B/CI66S
11UniProtVAR_006553N113KFA9_HUMANDisease (HEMB)  ---B/CN67K
12UniProtVAR_006554Y115CFA9_HUMANDisease (HEMB)  ---B/CY69C
13UniProtVAR_006555C119FFA9_HUMANDisease (HEMB)  ---B/CC73F
14UniProtVAR_006556C119RFA9_HUMANDisease (HEMB)  ---B/CC73R
15UniProtVAR_017347E124KFA9_HUMANDisease (HEMB)  ---B/CE78K
16UniProtVAR_006557G125EFA9_HUMANDisease (HEMB)  ---B/CG79E
17UniProtVAR_017348G125RFA9_HUMANDisease (HEMB)  ---B/CG79R
18UniProtVAR_006558G125VFA9_HUMANDisease (HEMB)  ---B/CG79V

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

(-) PROSITE Motifs  (5, 8)

Asymmetric/Biological Unit (5, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EGF_3PS50026 EGF-like domain profile.FA9_HUMAN93-129
 
  2B:47-83
C:47-83
2EGF_CAPS01187 Calcium-binding EGF-like domain signature.FA9_HUMAN93-117
 
  2B:47-71
C:47-71
3ASX_HYDROXYLPS00010 Aspartic acid and asparagine hydroxylation site.FA9_HUMAN108-119
 
  2B:62-73
C:62-73
4EGF_1PS00022 EGF-like domain signature 1.FA9_HUMAN117-128
 
  2B:71-82
C:71-82
5EGF_2PS01186 EGF-like domain signature 2.FA9_HUMAN117-128
 
155-170
  2B:71-82
C:71-82
-

(-) Exons   (2, 4)

Asymmetric/Biological Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002180991bENSE00002195519X:138612917-13861301195FA9_HUMAN1-30300--
1.2bENST000002180992bENSE00000677287X:138619169-138619332164FA9_HUMAN30-84550--
1.3ENST000002180993ENSE00001173335X:138619521-13861954525FA9_HUMAN85-9392B:46-47
C:46-47
2
2
1.4aENST000002180994aENSE00001173327X:138623235-138623348114FA9_HUMAN93-131392B:47-84
C:47-84
38
38
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

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 B from PDB  Type:PROTEIN  Length:39
 aligned with FA9_HUMAN | P00740 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:39
                                   101       111       121         
            FA9_HUMAN    92 VDGDQCESNPCLNGGSCKDDINSYECWCPFGFEGKNCEL 130
               SCOP domains d1edmb_ B: Factor IX (IXa)              SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author ...............eeeee..eeeee............ Sec.struct. author
             SAPs(SNPs) (1) -G--PS---RR---D-S-N-SK-C---F----KE----- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------S------------R-----R----- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---------------------------------V----- SAPs(SNPs) (3)
                PROSITE (1) -EGF_CA  PDB: B:47-71     ------------- PROSITE (1)
                PROSITE (2) -EGF_3  PDB: B:47-83 UniProt: 93-129  - PROSITE (2)
                PROSITE (3) ----------------ASX_HYDROXYL----------- PROSITE (3)
                PROSITE (4) -------------------------EGF_2       -- PROSITE (4)
                PROSITE (5) -------------------------EGF_1       -- PROSITE (5)
           Transcript 1 (1) 1.------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -Exon 1.4a  PDB: B:47-84 [INCOMPLETE]   Transcript 1 (2)
                 1edm B  46 VDGDQCESNPCLNGGSCKDDINSYECWCPFGFEGKNCEL  84
                                    55        65        75         

Chain C from PDB  Type:PROTEIN  Length:39
 aligned with FA9_HUMAN | P00740 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:39
                                   101       111       121         
            FA9_HUMAN    92 VDGDQCESNPCLNGGSCKDDINSYECWCPFGFEGKNCEL 130
               SCOP domains d1edmc_ C: Factor IX (IXa)              SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author ...............eeee....eeee............ Sec.struct. author
             SAPs(SNPs) (1) -G--PS---RR---D-S-N-SK-C---F----KE----- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------S------------R-----R----- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---------------------------------V----- SAPs(SNPs) (3)
                PROSITE (1) -EGF_CA  PDB: C:47-71     ------------- PROSITE (1)
                PROSITE (2) -EGF_3  PDB: C:47-83 UniProt: 93-129  - PROSITE (2)
                PROSITE (3) ----------------ASX_HYDROXYL----------- PROSITE (3)
                PROSITE (4) -------------------------EGF_2       -- PROSITE (4)
                PROSITE (5) -------------------------EGF_1       -- PROSITE (5)
           Transcript 1 (1) 1.------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -Exon 1.4a  PDB: C:47-84 [INCOMPLETE]   Transcript 1 (2)
                 1edm C  46 VDGDQCESNPCLNGGSCKDDINSYECWCPFGFEGKNCEL  84
                                    55        65        75         

   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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1EDM)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B,C   (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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FA9_HUMAN | P007401cfh 1cfi 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 1EDM)