Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CALCIUM BINDING TO THERMITASE. CRYSTALLOGRAPHIC STUDIES OF THERMITASE AT 0, 5 AND 100 MM CALCIUM
 
Authors :  P. Gros, K. H. Kalk, W. G. J. Hol
Date :  26 Oct 90  (Deposition) - 15 Jan 92  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  E,I
Keywords :  Complex(Serine Proteinase-Inhibitor) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Gros, K. H. Kalk, W. G. Hol
Calcium Binding To Thermitase. Crystallographic Studies Of Thermitase At 0, 5, And 100 Mm Calcium.
J. Biol. Chem. V. 266 2953 1991
PubMed-ID: 1993669
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THERMITASE
    Chains: E
    EC Number: 3.4.21.66
    Engineered: YES
    Organism Scientific: THERMOACTINOMYCES VULGARIS
    Organism Taxid: 2026
 
Molecule 2 - EGLIN C
    Chains: I
    Engineered: YES
    Expression System: UNIDENTIFIED
    Expression System Taxid: 32644
    Organism Scientific: HIRUDINARIA MANILLENSIS
    Organism Taxid: 6419

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : EI

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
1AC1SOFTWAREASP E:5 , ASP E:47 , VAL E:82 , ASN E:85 , THR E:87 , ILE E:89BINDING SITE FOR RESIDUE CA E 343
2AC2SOFTWAREASP E:57 , ASP E:60 , ASP E:62 , THR E:64 , GLN E:66 , HOH E:430BINDING SITE FOR RESIDUE CA E 344
3AC3SOFTWAREVAL E:199 , ASP E:201 , HOH E:357 , HOH E:359 , HOH E:375 , HOH E:452BINDING SITE FOR RESIDUE CA E 345

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr E:171 -Pro E:172
2Pro E:214 -Thr E:215

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TEC)

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1POTATO_INHIBITORPS00285 Potato inhibitor I family signature.ICIC_HIRME10-21  1I:10-21
2SUBTILASE_ASPPS00136 Serine proteases, subtilase family, aspartic acid active site.THET_THEVU34-45  1E:34-45
3SUBTILASE_HISPS00137 Serine proteases, subtilase family, histidine active site.THET_THEVU71-81  1E:71-81
4SUBTILASE_SERPS00138 Serine proteases, subtilase family, serine active site.THET_THEVU223-233  1E:223-233

(-) Exons   (0, 0)

(no "Exon" information available for 3TEC)

(-) 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 E from PDB  Type:PROTEIN  Length:279
 aligned with THET_THEVU | P04072 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         
           THET_THEVU     1 YTPNDPYFSSRQYGPQKIQAPQAWDIAEGSGAKIAIVDTGVQSNHPDLAGKVVGGWDFVDNDSTPQNGNGHGTHCAGIAAAVTNNSTGIAGTAPKASILAVRVLDNSGSGTWTAVANGITYAADQGAKVISLSLGGTVGNSGLQQAVNYAWNKGSVVVAAAGNAGNTAPNYPAYYSNAIAVASTDQNDNKSSFSTYGSVVDVAAPGSWIYSTYPTSTYASLSGTSMATPHVAGVAGLLASQGRSASNIRAAIENTADKISGTGTYWAKGRVNAYKAVQY 279
               SCOP domains d3tece_ E: Thermitase                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 3tecE00 E:1-279  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------Peptidase_S8-3tecE01 E:33-278                                                                                                                                                                                                                         - Pfam domains
         Sec.struct. author ....hhhhhhh.hhhhhhhhhhhhh.......eeeeee.............eeeeee............hhhhhhhhhhhh...............eeeeee........hhhhhhhhhhhhhhh...eeee.ee....hhhhhhhhhhhhhhh.eeeee.................eeeeeee.................eeee...eeeee...eeeee.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.............ee.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------SUBTILASE_AS-------------------------SUBTILASE_H---------------------------------------------------------------------------------------------------------------------------------------------SUBTILASE_S---------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tec E   1 YTPNDPYFSSRQYGPQKIQAPQAWDIAEGSGAKIAIVDTGVQSNHPDLAGKVVGGWDFVDNDSTPQNGNGHGTHCAGIAAAVTNNSTGIAGTAPKASILAVRVLDNSGSGTWTAVANGITYAADQGAKVISLSLGGTVGNSGLQQAVNYAWNKGSVVVAAAGNAGNTAPNYPAYYSNAIAVASTDQNDNKSSFSTYGSVVDVAAPGSWIYSTYPTSTYASLSGTSMATPHVAGVAGLLASQGRSASNIRAAIENTADKISGTGTYWAKGRVNAYKAVQY 279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         


Chain I from PDB  Type:PROTEIN  Length:63
 aligned with ICIC_HIRME | P01051 from UniProtKB/Swiss-Prot  Length:70

    Alignment length:63
                                    17        27        37        47        57        67   
           ICIC_HIRME     8 KSFPEVVGKTVDQAREYFTLHYPQYDVYFLPEGSPVTLDLRYNRVRVFYNPGTNVVNHVPHVG  70
               SCOP domains d3teci_ I: Eglin C                                              SCOP domains
               CATH domains 3tecI00 I:8-70 Trypsin Inhibitor V, subunit A                   CATH domains
               Pfam domains potato_inhibit-3tecI01 I:8-70                                   Pfam domains
         Sec.struct. author ..hhhhh..hhhhhhhhhhhhh...eeeeee....ee......eeeeee.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --POTATO_INHIB------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 3tec I   8 KSFPEVVGKTVDQAREYFTLHYPQYDVYFLPEGSPVTLDLRYNRVRVFYNPGTNVVNHVPHVG  70
                                    17        27        37        47        57        67
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: CI-2 (32)
(-)
Clan: no clan defined [family: Peptidase_S8] (104)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E   (THET_THEVU | P04072)
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: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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    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.

Chain I   (ICIC_HIRME | P01051)
molecular function
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0009611    response to wounding    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 stimulus indicating damage to the organism.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro E:214 - Thr E:215   [ RasMol ]  
    Tyr E:171 - Pro E:172   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3tec
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ICIC_HIRME | P01051
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  THET_THEVU | P04072
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.21.66
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  ICIC_HIRME | P01051
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  THET_THEVU | P04072
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ICIC_HIRME | P01051: 1acb 1cse 1egl 1egp 1mee 1sbn 1sib 1tec 2sec 2tec 4b1t 4b2a 4b2b 4b2c 4h4f
        THET_THEVU | P04072: 1tec 1thm 2tec

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3TEC)