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 :  THE COMPLEX BETWEEN THE SUBTILISIN FROM A MESOPHILIC BACTERIUM AND THE LEECH INHIBITOR EGLIN-C
 
Authors :  Z. Dauter, C. Betzel, K. S. Wilson
Date :  15 Apr 91  (Deposition) - 15 Oct 92  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,I
Keywords :  Complex(Serine Proteinase-Inhibitor) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Dauter, C. Betzel, N. Genov, N. Pipon, K. S. Wilson
Complex Between The Subtilisin From A Mesophilic Bacterium And The Leech Inhibitor Eglin-C.
Acta Crystallogr. , Sect. B V. 47 707 1991
PubMed-ID: 1793542  |  Reference-DOI: 10.1107/S0108768191004202
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MESENTERICOPEPTIDASE
    Chains: A
    EC Number: 3.4.21.14
    Engineered: YES
    Organism Scientific: BACILLUS PUMILUS
    Organism Taxid: 1408
 
Molecule 2 - EGLIN C
    Chains: I
    Engineered: YES
    Organism Common: MEDICINAL LEECH
    Organism Scientific: HIRUDO MEDICINALIS
    Organism Taxid: 6421

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:2 , ASP A:41 , LEU A:75 , ASN A:77 , ILE A:79 , VAL A:81BINDING SITE FOR RESIDUE CA A 400
2AC2SOFTWAREALA A:169 , TYR A:171 , THR A:174 , HOH A:458BINDING SITE FOR RESIDUE CA A 401
3ACTAUTHORASP A:32 , HIS A:64 , SER A:221ENZYME ACTIVE SITE
4CA1AUTHORGLN A:2 , ASP A:41 , LEU A:75 , ASN A:77 , ILE A:79 , VAL A:81SITE WITH STRONG AFFINITY FOR THE CALCIUM ION
5CA2AUTHORALA A:169 , TYR A:171 , THR A:174 , HOH A:458SITE WITH WEAK AFFINITY FOR THE CALCIUM ION
6RSBAUTHORLEU I:45 , ASP I:46BINDING SITE OF THE EGLIN-C INHIBITOR

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:167 -Pro A:168

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MEE)

(-) 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.SUBT_BACPU28-39  1A:28-39
3SUBTILASE_HISPS00137 Serine proteases, subtilase family, histidine active site.SUBT_BACPU64-74  1A:64-74
4SUBTILASE_SERPS00138 Serine proteases, subtilase family, serine active site.SUBT_BACPU219-229  1A:219-229

(-) Exons   (0, 0)

(no "Exon" information available for 1MEE)

(-) 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 A from PDB  Type:PROTEIN  Length:275
 aligned with SUBT_BACPU | P07518 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:275
                                    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     
           SUBT_BACPU     1 AQSVPYGISQIKAPALHSQGYTGSNVKVAVIDSGIDSSHPDLNVRGGASFVPSETNPYQDGSSHGTHVAGTIAALNNSIGVLGVAPSSALYAVKVLDSTGSGQYSWIINGIEWAISNNMDVINMSLGGPTGSTALKTVVDKAVSSGIVVAAAAGNEGSSGSTSTVGYPAKYPSTIAVGAVNSANQRASFSSAGSELDVMAPGVSIQSTLPGGTYGAYNGTSMATPHVAGAAALILSKHPTWTNAQVRDRLESTATYLGSSFYYGKGLINVQAAAQ 275
               SCOP domains d1meea_ A: Messentericopeptidase                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1meeA00 A:1-275  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                                CATH domains
               Pfam domains --------------------------Peptidase_S8-1meeA01 A:27-275                                                                                                                                                                                                                             Pfam domains
         Sec.struct. author ...........hhhhhhhhhh....eeeeeee............eeeeee.............hhhhhhhhhh...............eeeeeee.......hhhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhhh.eeeeee.....................eeeeee................eeeeee..eeeee...eeeee......hhhhhhhhhhhhhhhh..hhhhhhhhhhhh............eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------SUBTILASE_AS------------------------SUBTILASE_H------------------------------------------------------------------------------------------------------------------------------------------------SUBTILASE_S---------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mee A   1 AQSVPYGISQIKAPALHSQGYTGSNVKVAVIDSGIDSSHPDLNVRGGASFVPSETNPYQDGSSHGTHVAGTIAALNNSIGVLGVAPSASLYAVKVLDSTGSGQYSWIINGIEWAISNNMDVINMSLGGPTGSTALKTVVDKAVSSGIVVAAAAGNEGSSGSTSTVGYPAKYPSTIAVGAVNSANQRASFSSAGSELDVMAPGVSIQSTLPGGTYGAYNGTSMATPHVAGAAALILSKHPTWTNAQVRDRLESTATYLGSSFYYGKGLINVQAAAQ 275
                                    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:64
 aligned with ICIC_HIRME | P01051 from UniProtKB/Swiss-Prot  Length:70

    Alignment length:64
                                    16        26        36        46        56        66    
           ICIC_HIRME     7 LKSFPEVVGKTVDQAREYFTLHYPQYDVYFLPEGSPVTLDLRYNRVRVFYNPGTNVVNHVPHVG  70
               SCOP domains d1meei_ I: Eglin C                                               SCOP domains
               CATH domains 1meeI00 I:7-70 Trypsin Inhibitor V, subunit A                    CATH domains
               Pfam domains potato_inhibit-1meeI01 I:7-70                                    Pfam domains
         Sec.struct. author ...........hhhhhhhhhhh.......................................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---POTATO_INHIB------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 1mee I   7 LKSFPEVVGKTVDQAREYFTLHYPQYNVYFLPEGSPVTLDLRYNRVRVFYNPGTNVVNHVPHVG  70
                                    16        26        36        46        56        66
   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  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SUBT_BACPU | P07518)
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.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
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 ]
    ACT  [ RasMol ]  +environment [ RasMol ]
    CA1  [ RasMol ]  +environment [ RasMol ]
    CA2  [ RasMol ]  +environment [ RasMol ]
    RSB  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Tyr A:167 - Pro A:168   [ 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
  1mee
    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
  SUBT_BACPU | P07518
    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)
  3.4.21.14
    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)
  SUBT_BACPU | P07518
    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 1sbn 1sib 1tec 2sec 2tec 3tec 4b1t 4b2a 4b2b 4b2c 4h4f

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1MEE)