Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - manually
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - manually
NMR Structure - manually  (Jmol Viewer)
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF THE T STATE OF TURKEY OVOMUCOID AT PH 2.5
 
Authors :  J. Song, M. Laskowski Jr. , M. A. Qasim, J. L. Markley
Date :  24 Jul 02  (Deposition) - 04 Sep 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Omtky3 Conformational Transition T State, Cis-Trans Isomerization, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Song, M. Laskowski Jr, M. A. Qasim, J. L. Markley
Two Conformational States Of Turkey Ovomucoid Third Domain At Low Ph: Three-Dimensional Structures, Internal Dynamics, And Interconversion Kinetics And Thermodynamics.
Biochemistry V. 42 6380 2003
PubMed-ID: 12767219  |  Reference-DOI: 10.1021/BI034053F
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OVOMUCOID
    Chains: A
    Engineered: YES
    Fragment: RESIDUES 130-185
    Mutation: YES
    Other Details: THE SEQUENCE FOR OVOMUCOID FRAGMENT WAS CHEMICALLY SYNTHESIZED. IT OCCURS NATURALLY IN MELEAGRIS GALLOPAVO (COMMON TURKEY).
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1M8C)

(-) Sites  (0, 0)

(no "Site" information available for 1M8C)

(-) SS Bonds  (3, 3)

NMR Structure
No.Residues
1A:8 -A:38
2A:16 -A:35
3A:24 -A:56

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1M8C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M8C)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KAZAL_2PS51465 Kazal domain profile.IOVO_MELOE2-56  1A:2-56
IOVO_CROCS2-56  1A:2-56
IOVO_MELGA63-128
1-62
131-185		  1-
-
A:2-56
2KAZAL_1PS00282 Kazal serine protease inhibitors family signature.IOVO_MELOE16-38  1A:16-38
IOVO_CROCS16-38  1A:16-38
IOVO_MELGA86-108
145-167		  1-
A:16-38

(-) Exons   (0, 0)

(no "Exon" information available for 1M8C)

(-) Sequences/Alignments

NMR Structure
   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:56
 aligned with IOVO_CROCS | P52245 from UniProtKB/Swiss-Prot  Length:56

    Alignment length:56
                                    10        20        30        40        50      
           IOVO_CROCS     1 LAAVSVDCSEYPKPACTLEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC  56
               SCOP domains d1m8ca_ A: Ovomucoid domains                             SCOP domains
               CATH domains 1m8cA00 A:1-56  [code=3.30.60.30, no name defined]       CATH domains
               Pfam domains -------Kazal_1-1m8cA01 A:8-56                            Pfam domains
         Sec.struct. author ......................eee....ee.hhhhhhhhhhhh.....eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -KAZAL_2  PDB: A:2-56 UniProt: 2-56                      PROSITE (1)
                PROSITE (2) -------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------- PROSITE (3)
                PROSITE (4) ---------------KAZAL_1  PDB: A:16-38  ------------------ PROSITE (4)
                 Transcript -------------------------------------------------------- Transcript
                 1m8c A   1 LAAVSVDCSEYPKDACTLEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC  56
                                    10        20        30        40        50      


Chain A from PDB  Type:PROTEIN  Length:56
 aligned with IOVO_MELGA | P68390 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:56
                                   139       149       159       169       179      
           IOVO_MELGA   130 LAAVSVDCSEYPKPACTLEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC 185
               SCOP domains d1m8ca_ A: Ovomucoid domains                             SCOP domains
               CATH domains 1m8cA00 A:1-56  [code=3.30.60.30, no name defined]       CATH domains
               Pfam domains -------Kazal_1-1m8cA01 A:8-56                            Pfam domains
         Sec.struct. author ......................eee....ee.hhhhhhhhhhhh.....eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------KAZAL_1  PDB: A:16-38  ------------------ PROSITE (2)
                PROSITE (3) -------------------------------------------------------- PROSITE (3)
                PROSITE (4) -------------------------------------------------------- PROSITE (4)
                PROSITE (5) -------------------------------------------------------- PROSITE (5)
                PROSITE (1) -KAZAL_2  PDB: A:2-56 UniProt: 131-185                   PROSITE (1)
                 Transcript -------------------------------------------------------- Transcript
                 1m8c A   1 LAAVSVDCSEYPKDACTLEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC  56
                                    10        20        30        40        50      


Chain A from PDB  Type:PROTEIN  Length:56
 aligned with IOVO_MELOE | P68436 from UniProtKB/Swiss-Prot  Length:56

    Alignment length:56
                                    10        20        30        40        50      
           IOVO_MELOE     1 LAAVSVDCSEYPKPACTLEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC  56
               SCOP domains d1m8ca_ A: Ovomucoid domains                             SCOP domains
               CATH domains 1m8cA00 A:1-56  [code=3.30.60.30, no name defined]       CATH domains
               Pfam domains -------Kazal_1-1m8cA01 A:8-56                            Pfam domains
         Sec.struct. author ......................eee....ee.hhhhhhhhhhhh.....eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -KAZAL_2  PDB: A:2-56 UniProt: 2-56                      PROSITE (2)
                PROSITE (3) ---------------KAZAL_1  PDB: A:16-38  ------------------ PROSITE (3)
                 Transcript -------------------------------------------------------- Transcript
                 1m8c A   1 LAAVSVDCSEYPKDACTLEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC  56
                                    10        20        30        40        50
   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, 1)

NMR Structure
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Kazal (46)

(-) Gene Ontology  (5, 15)

NMR Structure(hide GO term definitions)
Chain A   (IOVO_CROCS | P52245)
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.
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 A   (IOVO_MELOE | P68436)
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.
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 A   (IOVO_MELGA | P68390)
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.
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.

 Visualization

(-) Interactive Views

NMR Structure
  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
(no "Ligands, Modified Residues, Ions" information available for 1m8c)
 
  Sites
(no "Sites" information available for 1m8c)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1m8c)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models 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
  1m8c
    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
  IOVO_CROCS | P52245
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  IOVO_MELGA | P68390
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  IOVO_MELOE | P68436
    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)
  (no 'Enzyme Classificator' available)
    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
  IOVO_CROCS | P52245
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  IOVO_MELGA | P68390
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  IOVO_MELOE | P68436
    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
        IOVO_CROCS | P52245: 1m8b
        IOVO_MELGA | P68390: 1cho 1cso 1ct0 1ct2 1ct4 1ds2 1ds3 1hja 1m8b 1omt 1omu 1ppf 1r0r 1sgd 1sge 1sgn 1sgp 1sgq 1sgr 1sgy 1tur 1tus 1yu6 1z7k 2gkr 2gkt 2gkv 2nu0 2nu1 2nu2 2nu3 2nu4 2sgd 2sge 2sgf 2sgp 2sgq 3sgb 3sgq
        IOVO_MELOE | P68436: 1m8b 1ppf 2nu0 2nu1 2nu2 2nu3 2nu4

(-) Related Entries Specified in the PDB File

1m8b SOLUTION STRUCTURE OF THE C STATE OF TURKEY OVOMUCOID AT PH 2.5