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(-) Description

Title :  SUBSTRATE INDUCED REMODELING OF THE ACTIVE SITE REGULATES HTRA1 ACTIVITY
 
Authors :  L. Truebestein, A. Tennstaedt, P. Hauske, T. Krojer, M. Kaiser, T. Clau M. Ehrmann
Date :  16 Jul 10  (Deposition) - 23 Feb 11  (Release) - 30 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Serine Protease, Degp, Htra, Protease, Hydrolase-Peptide Inhibitor Complex, Hydrolase-Hydrolase Substrate Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Truebestein, A. Tennstaedt, T. Monig, T. Krojer, F. Canellas, M. Kaiser, T. Clausen, M. Ehrmann
Substrate-Induced Remodeling Of The Active Site Regulates Human Htra1 Activity.
Nat. Struct. Mol. Biol. V. 18 386 2011
PubMed-ID: 21297635  |  Reference-DOI: 10.1038/NSMB.2013

(-) Compounds

Molecule 1 - SERINE PROTEASE HTRA1
    ChainsA
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 158-480
    GeneHTRA1, HTRA, PRSS11
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymL56, SERINE PROTEASE 11
 
Molecule 2 - CITRATE SYNTHASE
    ChainsB
    EngineeredYES
    FragmentUNP RESIDUES 371-377
    Other DetailsPEPTIDYL BORONIC ACID INHIBITOR
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (3x)AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1B2V1Mod. Amino AcidVALINE BORONIC ACID
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1B2V3Mod. Amino AcidVALINE BORONIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:220 , LEU A:309 , ASN A:324 , TYR A:325 , GLY A:326 , ASN A:327 , SER A:328 , THR A:344 , LEU A:345 , LYS A:346BINDING SITE FOR CHAIN B OF CITRATE SYNTHASE

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NZI)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 8)

Asymmetric Unit (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076376R166LHTRA1_HUMANDisease (CADASIL2)864622781AR166L
2UniProtVAR_076377A173PHTRA1_HUMANDisease (CADASIL2)  ---AA173P
3UniProtVAR_063148A252THTRA1_HUMANDisease (CARASIL)113993968AA252T
4UniProtVAR_076378S284GHTRA1_HUMANDisease (CADASIL2)  ---AS284G
5UniProtVAR_076379S284RHTRA1_HUMANDisease (CADASIL2)864622782AS284R
6UniProtVAR_076380P285QHTRA1_HUMANDisease (CADASIL2)  ---AP285Q
7UniProtVAR_076381F286VHTRA1_HUMANDisease (CADASIL2)  ---AF286V
8UniProtVAR_063149V297MHTRA1_HUMANDisease (CARASIL)113993969AV297M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (8, 24)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076376R166LHTRA1_HUMANDisease (CADASIL2)864622781AR166L
2UniProtVAR_076377A173PHTRA1_HUMANDisease (CADASIL2)  ---AA173P
3UniProtVAR_063148A252THTRA1_HUMANDisease (CARASIL)113993968AA252T
4UniProtVAR_076378S284GHTRA1_HUMANDisease (CADASIL2)  ---AS284G
5UniProtVAR_076379S284RHTRA1_HUMANDisease (CADASIL2)864622782AS284R
6UniProtVAR_076380P285QHTRA1_HUMANDisease (CADASIL2)  ---AP285Q
7UniProtVAR_076381F286VHTRA1_HUMANDisease (CADASIL2)  ---AF286V
8UniProtVAR_063149V297MHTRA1_HUMANDisease (CARASIL)113993969AV297M

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.HTRA1_HUMAN365-454  1A:365-370
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.HTRA1_HUMAN365-454  3A:365-370

(-) Exons   (5, 5)

Asymmetric Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003689841aENSE00001448527chr10:124221041-124221640600HTRA1_HUMAN1-1581580--
1.2ENST000003689842ENSE00001727698chr10:124248418-124248517100HTRA1_HUMAN158-191341A:160-19132
1.3ENST000003689843ENSE00001656483chr10:124248938-124249142205HTRA1_HUMAN191-259691A:191-25969
1.4ENST000003689844ENSE00001691312chr10:124266207-124266401195HTRA1_HUMAN260-324651A:260-32465
1.5ENST000003689845ENSE00001099158chr10:124266886-12426691833HTRA1_HUMAN325-335111A:325-33511
1.6ENST000003689846ENSE00001099160chr10:124268172-124268286115HTRA1_HUMAN336-374391A:336-37035
1.7ENST000003689847ENSE00001099153chr10:124269612-12426966958HTRA1_HUMAN374-393200--
1.8ENST000003689848ENSE00001099157chr10:124271486-12427158196HTRA1_HUMAN393-425330--
1.9bENST000003689849bENSE00001608082chr10:124273707-124274424718HTRA1_HUMAN425-480560--

(-) 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:211
 aligned with HTRA1_HUMAN | Q92743 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:211
                                   169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369 
          HTRA1_HUMAN   160 EDPNSLRHKYNFIADVVEKIAPAVVHIELFRKLPFSKREVPVASGSGFIVSEDGLIVTNAHVVTNKHRVKVELKNGATYEAKIKDVDEKADIALIKIDHQGKLPVLLLGRSSELRPGEFVVAIGSPFSLQNTVTTGIVSTTQRGGKELGLRNSDMDYIQTDAIINYGNSGGPLVNLDGEVIGINTLKVTAGISFAIPSDKIKKFLTESHDR 370
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------Trypsin_2-3nziA01 A:204-342                                                                                                                ---------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh..eeeeeeeee......eeeeeeeeeee.....eeeeehhhhh...eeeee.........eeeeee....eeeee.............hhhhh....eeeeeehhhhh..eeeeeeeeeeeee.hhh.......eeeee...........eeee....eeeeeeeeee..eeeeeehhhhhhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) ------L------P------------------------------------------------------------------------------T-------------------------------GQV----------M------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------R-------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDZ    PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:160-191        --------------------------------------------------------------------Exon 1.4  PDB: A:260-324 UniProt: 260-324                        Exon 1.5   Exon 1.6  PDB: A:336-370            Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.3  PDB: A:191-259 UniProt: 191-259                            --------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3nzi A 160 EDPNSLRHKYNFIADVVEKIAPAVVHIELFRKLPFSKREVPVASGSGFIVSEDGLIVTNAHVVTNKHRVKVELKNGATYEAKIKDVDEKADIALIKIDHQGKLPVLLLGRSSELRPGEFVVAIGSPFSLQNTVTTGIVSTTQRGGKELGLRNSDMDYIQTDAIINYGNSGGPLVNLDGEVIGINTLKVTAGISFAIPSDKIKKFLTESHDR 370
                                   169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369 

Chain B from PDB  Type:PROTEIN  Length:5
 aligned with CISY_MOUSE | Q9CZU6 from UniProtKB/Swiss-Prot  Length:464

    Alignment length:5
           CISY_MOUSE   373 MFKLV 377
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains Citra Pfam domains
         Sec.struct. author ..ee. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 3nzi B   4 MFKLv   8
                                |
                                |
                                8-B2V

Chain B from PDB  Type:PROTEIN  Length:5
 aligned with Q80X68_MOUSE | Q80X68 from UniProtKB/TrEMBL  Length:466

    Alignment length:5
         Q80X68_MOUSE   373 MFKLV 377
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains Citra Pfam domains
         Sec.struct. author ..ee. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 3nzi B   4 MFKLv   8
                                |
                                8-B2V

   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  (0, 0)

(no "SCOP Domain" information available for 3NZI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit

(-) Gene Ontology  (35, 42)

Asymmetric Unit(hide GO term definitions)
Chain A   (HTRA1_HUMAN | Q92743)
molecular function
    GO:0019838    growth factor binding    Interacting selectively and non-covalently with any growth factor, proteins or polypeptides that stimulate a cell or organism to grow or proliferate.
    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:0005520    insulin-like growth factor binding    Interacting selectively and non-covalently with an insulin-like growth factor, any member of a group of polypeptides that are structurally homologous to insulin and share many of its biological activities, but are immunologically distinct from it.
    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:0060718    chorionic trophoblast cell differentiation    The process in which relatively unspecialized cells of the ectoplacental cone acquire specialized structural and/or functional features that characterize chorionic trophoblasts. These cells will migrate towards the spongiotrophoblast layer and give rise to syncytiotrophoblasts of the labyrinthine layer.
    GO:0097187    dentinogenesis    The process whose specific outcome is the formation of dentin, the mineralized tissue that constitutes the major bulk of teeth. Dentin may be one of three types: primary dentin, secondary dentin, and tertiary dentin.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0030514    negative regulation of BMP signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the BMP signaling pathway.
    GO:0050687    negative regulation of defense response to virus    Any process that stops, prevents or reduces the rate or extent of antiviral mechanisms, thereby facilitating viral replication.
    GO:0030512    negative regulation of transforming growth factor beta receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of any TGF-beta receptor signaling pathway.
    GO:0001890    placenta development    The process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
    GO:0050679    positive regulation of epithelial cell proliferation    Any process that activates or increases the rate or extent of epithelial cell proliferation.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0001558    regulation of cell growth    Any process that modulates the frequency, rate, extent or direction of cell growth.
cellular component
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

Chain B   (Q80X68_MOUSE | Q80X68)
molecular function
    GO:0004108    citrate (Si)-synthase activity    Catalysis of the reaction: acetyl-CoA + H2O + oxaloacetate = citrate + CoA, where the acetyl group is added to the si-face of oxaloacetate; acetyl-CoA thus provides the two carbon atoms of the pro-S carboxymethyl group.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0046912    transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor), with the acyl group being converted into alkyl on transfer.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0006101    citrate metabolic process    The chemical reactions and pathways involving citrate, 2-hydroxy-1,2,3-propanetricarboyxlate. Citrate is widely distributed in nature and is an important intermediate in the TCA cycle and the glyoxylate cycle.
    GO:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
cellular component
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Chain B   (CISY_MOUSE | Q9CZU6)
molecular function
    GO:0004108    citrate (Si)-synthase activity    Catalysis of the reaction: acetyl-CoA + H2O + oxaloacetate = citrate + CoA, where the acetyl group is added to the si-face of oxaloacetate; acetyl-CoA thus provides the two carbon atoms of the pro-S carboxymethyl group.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0046912    transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor), with the acyl group being converted into alkyl on transfer.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0006101    citrate metabolic process    The chemical reactions and pathways involving citrate, 2-hydroxy-1,2,3-propanetricarboyxlate. Citrate is widely distributed in nature and is an important intermediate in the TCA cycle and the glyoxylate cycle.
    GO:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
cellular component
    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:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HTRA1_HUMAN | Q927432joa 2ytw 3num 3nwu 3tjn 3tjo 3tjq

(-) Related Entries Specified in the PDB File

3num 3nwu