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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MITOCHONDRIAL SERINE PROTEASE HTRA2
 
Authors :  W. Li, S. M. Srinivasula, J. Chai, P. Li, J. W. Wu, Z. Zhang, E. S. Alnemri,
Date :  07 Apr 02  (Deposition) - 22 May 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (3x)
Keywords :  Apoptosis, Serine Protease, Pdz Domain, Caspase Activation, Iap- Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Li, S. M. Srinivasula, J. Chai, P. Li, J. W. Wu, Z. Zhang, E. S. Alnemri Y. Shi
Structural Insights Into The Pro-Apoptotic Function Of Mitochondrial Serine Protease Htra2/Omi.
Nat. Struct. Biol. V. 9 436 2002
PubMed-ID: 11967569  |  Reference-DOI: 10.1038/NSB795

(-) Compounds

Molecule 1 - HTRA2 SERINE PROTEASE
    ChainsA
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21B
    Expression System Taxid562
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (3x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1LCY)

(-) Sites  (0, 0)

(no "Site" information available for 1LCY)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LCY)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_027349A141SHTRA2_HUMANPolymorphism72470544AA8S
2UniProtVAR_076969A227SHTRA2_HUMANPolymorphism375322953AA94S
3UniProtVAR_027350G399SHTRA2_HUMANPolymorphism72470545AG266S
4UniProtVAR_077961R404QHTRA2_HUMANDisease (MGCA8)767006508AR271Q
5UniProtVAR_046135R404WHTRA2_HUMANDisease (PARK13)  ---AR271W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_027349A141SHTRA2_HUMANPolymorphism72470544AA8S
2UniProtVAR_076969A227SHTRA2_HUMANPolymorphism375322953AA94S
3UniProtVAR_027350G399SHTRA2_HUMANPolymorphism72470545AG266S
4UniProtVAR_077961R404QHTRA2_HUMANDisease (MGCA8)767006508AR271Q
5UniProtVAR_046135R404WHTRA2_HUMANDisease (PARK13)  ---AR271W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (5, 15)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_027349A141SHTRA2_HUMANPolymorphism72470544AA8S
2UniProtVAR_076969A227SHTRA2_HUMANPolymorphism375322953AA94S
3UniProtVAR_027350G399SHTRA2_HUMANPolymorphism72470545AG266S
4UniProtVAR_077961R404QHTRA2_HUMANDisease (MGCA8)767006508AR271Q
5UniProtVAR_046135R404WHTRA2_HUMANDisease (PARK13)  ---AR271W

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.HTRA2_HUMAN390-445  1A:257-312
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.HTRA2_HUMAN390-445  1A:257-312
Biological Unit 2 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.HTRA2_HUMAN390-445  3A:257-312

(-) Exons   (8, 8)

Asymmetric Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002580801aENSE00001276828chr2:74756504-747576391136HTRA2_HUMAN1-1691691A:6-3631
1.2cENST000002580802cENSE00000763573chr2:74757744-74757948205HTRA2_HUMAN169-237691A:36-10469
1.3aENST000002580803aENSE00000763626chr2:74758038-74758232195HTRA2_HUMAN238-302651A:105-169 (gaps)65
1.3dENST000002580803dENSE00001276808chr2:74758466-7475849833HTRA2_HUMAN303-313111A:170-18011
1.3iENST000002580803iENSE00000920847chr2:74758724-74758829106HTRA2_HUMAN314-349361A:181-21030
1.3jENST000002580803jENSE00001276754chr2:74758983-7475905270HTRA2_HUMAN349-372241A:226-23914
1.4ENST000002580804ENSE00001276734chr2:74759746-7475984196HTRA2_HUMAN372-404331A:239-27133
1.5fENST000002580805fENSE00000920849chr2:74759947-74760472526HTRA2_HUMAN404-458551A:271-32555

(-) 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:296
 aligned with HTRA2_HUMAN | O43464 from UniProtKB/Swiss-Prot  Length:458

    Alignment length:320
                                   148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458
          HTRA2_HUMAN   139 PPASPRSQYNFIADVVEKTAPAVVYIEILDRHPFLGREVPISNGSGFVVAADGLIVTNAHVVADRRRVRVRLLSGDTYEAVVTAVDPVADIATLRIQTKEPLPTLPLGRSADVRQGEFVVAMGSPFALQNTITSGIVSSAQRPARDLGLPQTNVEYIQTDAAIDFGNSGGPLVNLDGEVIGVNTMKVTAGISFAIPSDRLREFLHRGEKKNSSSGISGSQRRYIGVMMLTLSPSILAELQLREPSFPDVQHGVLIHKVILGSPAHRAGLRPGDVILAIGEQMVQNAEDVYEAVRTQSQLAVQIRRGRETLTLYVTPEVTE 458
               SCOP domains d1lcya2 A:6-210 Mitochondrial serine protease HtrA2, catalytic domain                                                                                                                                                       d1lcya1 A:226-325 Mitochondrial serine protease HtrA2                                                SCOP domains
               CATH domains 1lcyA01 A:6-109,A:204-210 Trypsin-like serine proteases                                                 1lcyA02 A:110-202 Trypsin-like serine p         roteases                                     -1lcyA01               -1lcyA03 A:227-323  [code=2.30.42.10, no name defined]                                            -- CATH domains
               Pfam domains -------------------------------------------Trypsin_2-1lcyA02 A:49-187                                                                                                                 -----------------------               -PDZ_2-1lcyA01 A:227-320                                                                       ----- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh..eeeeeeeeee....eeeeeeeeeeeeee...eeeehhhhhh...eeeee.....eeeeeeeeee....eeeee.............hhhhh....eeee...........eeee.......---------....eee...........eeee....eeeeeeeeee..eeeeeehhhhhhhh.---------------.ee..eeeee.hhhhhhhhh............eeeeee...hhhhhhh.....eeeee..ee..hhhhhhhhhh....eeeeeee..eeeeeee..ee.. Sec.struct. author
             SAPs(SNPs) (1) --S-------------------------------------------------------------------------------------S---------------------------------------------------------------------------------------------------------------------------------------------------------------------------S----Q------------------------------------------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDZ  PDB: A:257-312 UniProt: 390-445                    ------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:6-36         --------------------------------------------------------------------Exon 1.3a  PDB: A:105-169 (gaps) UniProt: 238-302                Exon 1.3d  Exon 1.3i  PDB: A:181-210           ----------------------Exon 1.4  PDB: A:239-271         ------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.2c  PDB: A:36-104 UniProt: 169-237                            ---------------------------------------------------------------------------------------------------------------Exon 1.3j  PDB: A:226-23-------------------------------Exon 1.5f  PDB: A:271-325 UniProt: 404-458              Transcript 1 (2)
                 1lcy A   6 PPASPRSQYNFIADVVEKTAPAVVYIEILDRHPFLGREVPISNGSGFVVAADGLIVTNAHVVADRRRVRVRLLSGDTYEAVVTAVDPVADIATLRIQTKEPLPTLPLGRSADVRQGEFVVAMGSPFALQNTITSGIVSSAQRP---------NVEYIQTDAAIDFGNAGGPLVNLDGEVIGVNTMKVTAGISFAIPSDRLREFLH---------------RRYIGVMMLTLSPSILAELQLREPSFPDVQHGVLIHKVILGSPAHRAGLRPGDVILAIGEQMVQNAEDVYEAVRTQSQLAVQIRRGRETLTLYVTPEVTE 325
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145  |      -  |    165       175       185       195       205    |    -         -|      235       245       255       265       275       285       295       305       315       325
                                                                                                                                                                        148       158                                                 210             226                                                                                                   

   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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (2, 3)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: PDZ-like (184)

(-) Gene Ontology  (51, 51)

Asymmetric Unit(hide GO term definitions)
Chain A   (HTRA2_HUMAN | O43464)
molecular function
    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: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: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: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).
    GO:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
biological process
    GO:0008344    adult locomotory behavior    Locomotory behavior in a fully developed and mature organism.
    GO:0007628    adult walking behavior    The behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0044257    cellular protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by individual cells.
    GO:0071363    cellular response to growth factor stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus.
    GO:0034605    cellular response to heat    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
    GO:0035458    cellular response to interferon-beta    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-beta stimulus. Interferon-beta is a type I interferon.
    GO:0034599    cellular response to oxidative stress    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0071300    cellular response to retinoic acid    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus.
    GO:0006672    ceramide metabolic process    The chemical reactions and pathways involving ceramides, any N-acylated sphingoid.
    GO:0097194    execution phase of apoptosis    A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0030900    forebrain development    The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
    GO:0097193    intrinsic apoptotic signaling pathway    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway starts with reception of an intracellular signal (e.g. DNA damage, endoplasmic reticulum stress, oxidative stress etc.), and ends when the execution phase of apoptosis is triggered. The intrinsic apoptotic signaling pathway is crucially regulated by permeabilization of the mitochondrial outer membrane (MOMP).
    GO:0008630    intrinsic apoptotic signaling pathway in response to DNA damage    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the detection of DNA damage, and ends when the execution phase of apoptosis is triggered.
    GO:0007005    mitochondrion organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
    GO:0045786    negative regulation of cell cycle    Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
    GO:0060548    negative regulation of cell death    Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
    GO:1901215    negative regulation of neuron death    Any process that stops, prevents or reduces the frequency, rate or extent of neuron death.
    GO:1902176    negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of an oxidative stress-induced intrinsic apoptotic signaling pathway.
    GO:0048666    neuron development    The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
    GO:0019742    pentacyclic triterpenoid metabolic process    The chemical reactions and pathways involving pentacyclic triterpenoid compounds, terpenoids with six isoprene units and 5 carbon rings.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0010942    positive regulation of cell death    Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
    GO:0043280    positive regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that activates or increases the activity of a cysteine-type endopeptidase involved in the apoptotic process.
    GO:2001269    positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of cysteine-type endopeptidase activity involved in apoptotic signaling pathway.
    GO:2001241    positive regulation of extrinsic apoptotic signaling pathway in absence of ligand    Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway in absence of ligand.
    GO:1903955    positive regulation of protein targeting to mitochondrion    Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
    GO:0016540    protein autoprocessing    Processing which a protein carries out itself. This involves actions such as the autolytic removal of residues to generate the mature form of the protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:1903146    regulation of mitophagy    Any process that modulates the frequency, rate or extent of mitochondrion degradation (mitophagy).
    GO:0040014    regulation of multicellular organism growth    Any process that modulates the frequency, rate or extent of growth of the body of an organism so that it reaches its usual body size.
    GO:0009635    response to herbicide    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a herbicide stimulus. Herbicides are chemicals used to kill or control the growth of plants.
cellular component
    GO:0035631    CD40 receptor complex    A protein complex that contains at least CD40 (a cell surface receptor of the tumour necrosis factor receptor (TNFR) superfamily), and other signaling molecules.
    GO:0000785    chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
    GO:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0031966    mitochondrial membrane    Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.
    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
        HTRA2_HUMAN | O434642pzd 5fht

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