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(-) Description

Title :  HTRA1 CATALYTIC DOMAIN, APO FORM
 
Authors :  C. Eigenbrot, M. Ultsch
Date :  24 Aug 11  (Deposition) - 16 May 12  (Release) - 27 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,D
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
Biol. Unit 3:  D  (3x)
Keywords :  Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Eigenbrot, M. Ultsch, M. T. Lipari, P. Moran, S. J. Lin, R. Ganesan, C. Quan, J. Tom, W. Sandoval, M. Van Lookeren Campagne, D. Kirchhofe
Structural And Functional Analysis Of Htra1 And Its Subdomains.
Structure V. 20 1040 2012
PubMed-ID: 22578544  |  Reference-DOI: 10.1016/J.STR.2012.03.021

(-) Compounds

Molecule 1 - SERINE PROTEASE HTRA1
    ChainsA, B, D
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentPROTEASE DOMAIN (UNP RESIDUES 161-367)
    GeneHTRA, HTRA1, PRSS11
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHIGH-TEMPERATURE REQUIREMENT A SERINE PEPTIDASE 1, L56, SERINE PROTEASE 11

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABD
Biological Unit 1 (3x)A  
Biological Unit 2 (3x) B 
Biological Unit 3 (3x)  D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3TJN)

(-) Sites  (0, 0)

(no "Site" information available for 3TJN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 24)

Asymmetric Unit (8, 24)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076376R166LHTRA1_HUMANDisease (CADASIL2)864622781A/B/DR166L
2UniProtVAR_076377A173PHTRA1_HUMANDisease (CADASIL2)  ---A/B/DA173P
3UniProtVAR_063148A252THTRA1_HUMANDisease (CARASIL)113993968A/B/DA252T
4UniProtVAR_076378S284GHTRA1_HUMANDisease (CADASIL2)  ---A/B/DS284G
5UniProtVAR_076379S284RHTRA1_HUMANDisease (CADASIL2)864622782A/B/DS284R
6UniProtVAR_076380P285QHTRA1_HUMANDisease (CADASIL2)  ---A/B/DP285Q
7UniProtVAR_076381F286VHTRA1_HUMANDisease (CADASIL2)  ---A/B/DF286V
8UniProtVAR_063149V297MHTRA1_HUMANDisease (CARASIL)113993969A/B/DV297M

  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)
Biological Unit 2 (8, 24)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076376R166LHTRA1_HUMANDisease (CADASIL2)864622781BR166L
2UniProtVAR_076377A173PHTRA1_HUMANDisease (CADASIL2)  ---BA173P
3UniProtVAR_063148A252THTRA1_HUMANDisease (CARASIL)113993968BA252T
4UniProtVAR_076378S284GHTRA1_HUMANDisease (CADASIL2)  ---BS284G
5UniProtVAR_076379S284RHTRA1_HUMANDisease (CADASIL2)864622782BS284R
6UniProtVAR_076380P285QHTRA1_HUMANDisease (CADASIL2)  ---BP285Q
7UniProtVAR_076381F286VHTRA1_HUMANDisease (CADASIL2)  ---BF286V
8UniProtVAR_063149V297MHTRA1_HUMANDisease (CARASIL)113993969BV297M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (8, 24)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076376R166LHTRA1_HUMANDisease (CADASIL2)864622781DR166L
2UniProtVAR_076377A173PHTRA1_HUMANDisease (CADASIL2)  ---DA173P
3UniProtVAR_063148A252THTRA1_HUMANDisease (CARASIL)113993968DA252T
4UniProtVAR_076378S284GHTRA1_HUMANDisease (CADASIL2)  ---DS284G
5UniProtVAR_076379S284RHTRA1_HUMANDisease (CADASIL2)864622782DS284R
6UniProtVAR_076380P285QHTRA1_HUMANDisease (CADASIL2)  ---DP285Q
7UniProtVAR_076381F286VHTRA1_HUMANDisease (CADASIL2)  ---DF286V
8UniProtVAR_063149V297MHTRA1_HUMANDisease (CARASIL)113993969DV297M

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

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.HTRA1_HUMAN365-454
 
 
  3A:365-367
B:365-367
D:365-367
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.HTRA1_HUMAN365-454
 
 
  3A:365-367
-
-
Biological Unit 2 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.HTRA1_HUMAN365-454
 
 
  3-
B:365-367
-
Biological Unit 3 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.HTRA1_HUMAN365-454
 
 
  3-
-
D:365-367

(-) Exons   (5, 15)

Asymmetric Unit (5, 15)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003689841aENSE00001448527chr10:124221041-124221640600HTRA1_HUMAN1-1581580--
1.2ENST000003689842ENSE00001727698chr10:124248418-124248517100HTRA1_HUMAN158-191343A:164-191
B:163-191
D:164-191
28
29
28
1.3ENST000003689843ENSE00001656483chr10:124248938-124249142205HTRA1_HUMAN191-259693A:191-259
B:191-259
D:191-258
69
69
68
1.4ENST000003689844ENSE00001691312chr10:124266207-124266401195HTRA1_HUMAN260-324653A:260-324 (gaps)
B:260-324 (gaps)
D:262-324 (gaps)
65
65
63
1.5ENST000003689845ENSE00001099158chr10:124266886-12426691833HTRA1_HUMAN325-335113A:325-335
B:325-335
D:329-335
11
11
7
1.6ENST000003689846ENSE00001099160chr10:124268172-124268286115HTRA1_HUMAN336-374393A:336-367
B:336-367
D:336-367 (gaps)
32
32
32
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:190
 aligned with HTRA1_HUMAN | Q92743 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:204
                                   173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363    
          HTRA1_HUMAN   164 SLRHKYNFIADVVEKIAPAVVHIELFRKLPFSKREVPVASGSGFIVSEDGLIVTNAHVVTNKHRVKVELKNGATYEAKIKDVDEKADIALIKIDHQGKLPVLLLGRSSELRPGEFVVAIGSPFSLQNTVTTGIVSTTQRGGKELGLRNSDMDYIQTDAIINYGNSGGPLVNLDGEVIGINTLKVTAGISFAIPSDKIKKFLTES 367
               SCOP domains d3tjna_ A: automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..eeeeeeee........eeeeeeeeee.....eeeeehhhhh...eeeee.....eeeeeeeeee....eeeee.............hhhhh....eeeeeeeee..eeeeeeeeeee.--------------..eee...........eeee....eeeeeeeeee..eeeeeehhhhhhhhhh. 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:164-191    --------------------------------------------------------------------Exon 1.4  PDB: A:260-324 (gaps) UniProt: 260-324                 Exon 1.5   Exon 1.6  PDB: A:336-367         Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.3  PDB: A:191-259 UniProt: 191-259                            ------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3tjn A 164 SLRHKYNFIADVVEKIAPAVVHIELFRKLPFSKREVPVASGSGFIVSEDGLIVTNAHVVTNKHRVKVELKNGATYEAKIKDVDEKADIALIKIDHQGKLPVLLLGRSSELRPGEFVVAIGSPFSLQNTVTTGIVSTT--------------DYIQTDAIINYGNSGGPLVNLDGEVIGINTLKVTAGISFAIPSDKIKKFLTES 367
                                   173       183       193       203       213       223       233       243       253       263       273       283       293      |  -         - |     323       333       343       353       363    
                                                                                                                                                                  300            315                                                    

Chain B from PDB  Type:PROTEIN  Length:197
 aligned with HTRA1_HUMAN | Q92743 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:205
                                   172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362     
          HTRA1_HUMAN   163 NSLRHKYNFIADVVEKIAPAVVHIELFRKLPFSKREVPVASGSGFIVSEDGLIVTNAHVVTNKHRVKVELKNGATYEAKIKDVDEKADIALIKIDHQGKLPVLLLGRSSELRPGEFVVAIGSPFSLQNTVTTGIVSTTQRGGKELGLRNSDMDYIQTDAIINYGNSGGPLVNLDGEVIGINTLKVTAGISFAIPSDKIKKFLTES 367
               SCOP domains d3tjnb_ B: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..eeeeeeee........eeeeeeeeee.....eeeeehhhhh...eeeee.....eee.eeeeee....eeeee.............hhhhh....eeeeeehhhhh..eeeeeeeeeeeee..--------.eeeee...........eeee....eeeeeeeeee..eeeeeehhhhhhhhhhh 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: B:163-191     --------------------------------------------------------------------Exon 1.4  PDB: B:260-324 (gaps) UniProt: 260-324                 Exon 1.5   Exon 1.6  PDB: B:336-367         Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.3  PDB: B:191-259 UniProt: 191-259                            ------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3tjn B 163 NSLRHKYNFIADVVEKIAPAVVHIELFRKLPFSKREVPVASGSGFIVSEDGLIVTNAHVVTNKHRVKVELKNGATYEAKIKDVDEKADIALIKIDHQGKLPVLLLGRSSELRPGEFVVAIGSPFSLQNTVTTGIVSTTQRGGK--------MDYIQTDAIINYGNSGGPLVNLDGEVIGINTLKVTAGISFAIPSDKIKKFLTES 367
                                   172       182       192       202       212       222       232       242       252       262       272       282       292       302  |      - |     322       332       342       352       362     
                                                                                                                                                                        305      314                                                     

Chain D from PDB  Type:PROTEIN  Length:187
 aligned with HTRA1_HUMAN | Q92743 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:204
                                   173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363    
          HTRA1_HUMAN   164 SLRHKYNFIADVVEKIAPAVVHIELFRKLPFSKREVPVASGSGFIVSEDGLIVTNAHVVTNKHRVKVELKNGATYEAKIKDVDEKADIALIKIDHQGKLPVLLLGRSSELRPGEFVVAIGSPFSLQNTVTTGIVSTTQRGGKELGLRNSDMDYIQTDAIINYGNSGGPLVNLDGEVIGINTLKVTAGISFAIPSDKIKKFLTES 367
               SCOP domains d3tjnd_ D: automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..eeeeeeeee......eeeeeeeeeee.....eeeeehhhhh...eeeee.....eee.eeeeee....eeeee...---................eeeeee.......eeeeee.........--------...eee.....----..eeee....eeeee.--.....eeeeehhhhhhhhhh. 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: D:164-191    --------------------------------------------------------------------Exon 1.4  PDB: D:262-324 (gaps) UniProt: 260-324 [INCOMPLETE]    Exon 1.5   Exon 1.6  PDB: D:336-367 (gaps)  Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.3  PDB: D:191-258 UniProt: 191-259 [INCOMPLETE]               ------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3tjn D 164 SLRHKYNFIADVVEKIAPAVVHIELFRKLPFSKREVPVASGSGFIVSEDGLIVTNAHVVTNKHRVKVELKNGATYEAKIKDVDEKADIALIKIDH---LPVLLLGRSSELRPGEFVVAIGSPFSLQNTVTTGIVSTTQRGGK--------MDYIQTDAIIN----GGPLVNLDGEVIGINT--VTAGISFAIPSDKIKKFLTES 367
                                   173       183       193       203       213       223       233       243       253    |  263       273       283       293       303 |       -|      323|    | 333       343|  |   353       363    
                                                                                                                        258 262                                        305      314       324  329            344  |                    
                                                                                                                                                                                                                 347                    

   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, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TJN)

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,B,D   (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.

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3tjo 3tjq