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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-TERMINALLY TRUNCATED OMTKY3-DEL(1-5)
 
Authors :  T. W. Lee, M. A. Qasim, M. Laskowski Jr. , M. N. G. James
Date :  03 Apr 06  (Deposition) - 13 Feb 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.16
Chains :  Asym./Biol. Unit :  I
Keywords :  Reactive-Site Loop, Alpha-Helix, Antiparallel Beta-Sheet, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. W. Lee, M. A. Qasim, M. Laskowski, M. N. James
Structural Insights Into The Non-Additivity Effects In The Sequence-To-Reactivity Algorithm For Serine Peptidases And Their Inhibitors.
J. Mol. Biol. V. 367 527 2007
PubMed-ID: 17266986  |  Reference-DOI: 10.1016/J.JMB.2007.01.008
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OVOMUCOID
    Chains: I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: TURKEY OVOMUCOID THIRD DOMAIN, DEL (1-5)
    Organism Common: TURKEY
    Organism Scientific: MELEAGRIS GALLOPAVO
    Organism Taxid: 9103

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : I

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL I:6 , LEU I:50 , LYS I:55BINDING SITE FOR RESIDUE CL I 101

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1I:8 -I:38
2I:16 -I:35
3I:24 -I:56

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr I:11 -Pro I:12

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GKR)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KAZAL_1PS00282 Kazal serine protease inhibitors family signature.IOVO_MELGA86-108
145-167		  1-
I:16-38

(-) Exons   (0, 0)

(no "Exon" information available for 2GKR)

(-) 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 I from PDB  Type:PROTEIN  Length:51
 aligned with IOVO_MELGA | P68390 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:51
                                   144       154       164       174       184 
           IOVO_MELGA   135 VDCSEYPKPACTLEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC 185
               SCOP domains d2gkri_ I: automated matches                        SCOP domains
               CATH domains 2gkrI00 I:6-56  [code=3.30.60.30, no name defined]  CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author .................eee....ee.hhhhhhhhhhhh.....eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------KAZAL_1  PDB: I:16-38  ------------------ PROSITE
                 Transcript --------------------------------------------------- Transcript
                 2gkr I   6 VDCSEYPKPACTLEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC  56
                                    15        25        35        45        55
   Legend:   → Mismatch (orange background)
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  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)

Asymmetric/Biological Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GKR)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain I   (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.

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  2gkr
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 Related Entries

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

UniProtKB/Swiss-Prot
        IOVO_MELGA | P68390: 1cho 1cso 1ct0 1ct2 1ct4 1ds2 1ds3 1hja 1m8b 1m8c 1omt 1omu 1ppf 1r0r 1sgd 1sge 1sgn 1sgp 1sgq 1sgr 1sgy 1tur 1tus 1yu6 1z7k 2gkt 2gkv 2nu0 2nu1 2nu2 2nu3 2nu4 2sgd 2sge 2sgf 2sgp 2sgq 3sgb 3sgq

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2GKR)