Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  ATOMIC RESOLUTION STRUCTURE OF SQUASH TRYPSIN INHIBITOR: UNEXPECTED METAL COORDINATION
 
Authors :  R. Thaimattam, E. Tykarska, A. Bierzynski, G. M. Sheldrick, M. Jaskols
Date :  21 May 02  (Deposition) - 28 Aug 02  (Release) - 20 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.03
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Serine Protease Inhibitor, Metal Coordination, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Thaimattam, E. Tykarska, A. Bierzynski, G. M. Sheldrick, M. Jaskolski
Atomic Resolution Structure Of Squash Trypsin Inhibitor: Unexpected Metal Coordination.
Acta Crystallogr. , Sect. D V. 58 1448 2002
PubMed-ID: 12198301  |  Reference-DOI: 10.1107/S0907444902011769
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRYPSIN INHIBITOR I
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAED4
    Expression System Strain: BL21(DE3)-PLYS(S)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: WINTER SQUASH
    Organism Scientific: CUCURBITA MAXIMA
    Organism Taxid: 3661
    Synonym: CMTI-I

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3SO41Ligand/IonSULFATE ION
4ZN1Ligand/IonZINC ION
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MRD2Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3SO42Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:19 , GLU B:19BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWAREARG A:1 , HOH A:357 , GLU B:19 , HOH B:347BINDING SITE FOR RESIDUE SO4 B 205
3AC3SOFTWAREARG B:5 , ASP B:15 , CYS B:28 , GLY B:29 , GOL B:203 , HOH B:325BINDING SITE FOR RESIDUE MRD B 204
4AC4SOFTWARECYS A:3 , PRO A:4 , ARG A:5 , SER A:14 , ASP A:15 , CYS A:28 , HOH A:310 , HOH A:368BINDING SITE FOR RESIDUE GOL A 202
5AC5SOFTWAREILE A:6 , GLU B:9 , MRD B:204 , HOH B:371BINDING SITE FOR RESIDUE GOL B 203

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:3 -A:20
2A:10 -A:22
3A:16 -A:28
4B:3 -B:20
5B:10 -B:22
6B:16 -B:28

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LU0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LU0)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SQUASH_INHIBITORPS00286 Squash family of serine protease inhibitors signature.ITR1_CUCMA3-22
 		  2A:3-22
B:3-22
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SQUASH_INHIBITORPS00286 Squash family of serine protease inhibitors signature.ITR1_CUCMA3-22
 		  4A:3-22
B:3-22

(-) Exons   (0, 0)

(no "Exon" information available for 1LU0)

(-) 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:29
 aligned with ITR1_CUCMA | P01074 from UniProtKB/Swiss-Prot  Length:29

    Alignment length:29
                                    10        20         
            ITR1_CUCMA    1 RVCPRILMECKKDSDCLAECVCLEHGYCG 29
               SCOP domains d1lu0a_ A: Trypsin inhibitor  SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author ...........hhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE --SQUASH_INHIBITOR    ------- PROSITE
                 Transcript ----------------------------- Transcript
                  1lu0 A  1 RVCPRILLECKKDSDCLAECVCLEHGYCG 29
                                    10        20         


Chain B from PDB  Type:PROTEIN  Length:29
 aligned with ITR1_CUCMA | P01074 from UniProtKB/Swiss-Prot  Length:29

    Alignment length:29
                                    10        20         
            ITR1_CUCMA    1 RVCPRILMECKKDSDCLAECVCLEHGYCG 29
               SCOP domains d1lu0b_ B: Trypsin inhibitor  SCOP domains
               CATH domains ----------------------------- CATH domains
           Pfam domains (1) Squash-1lu0B01 B:1-29         Pfam domains (1)
           Pfam domains (2) Squash-1lu0B02 B:1-29         Pfam domains (2)
         Sec.struct. author ...........hhhhh....ee.....ee Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE --SQUASH_INHIBITOR    ------- PROSITE
                 Transcript ----------------------------- Transcript
                  1lu0 B  1 RVCPRILLECKKDSDCLAECVCLEHGYCG 29
                                    10        20
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1LU0)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Pept_Inhib_IE (9)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ITR1_CUCMA | P01074)
molecular function
    GO:0004866    endopeptidase inhibitor activity    Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
    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

Asymmetric 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MRD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1lu0)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  1lu0
    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
  ITR1_CUCMA | P01074
    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
  ITR1_CUCMA | P01074
    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
        ITR1_CUCMA | P01074: 1cti 1ppe 2cti 2sta 2v1v 3cti

(-) Related Entries Specified in the PDB File

1bxj 1BXJ IS NMR STRUCTURE OF THE SAME PROTEIN
1ppe 1PPE IS WILD TYPE SEQUENCE OF THE SAME PROTEIN COMPLEXED WITH BOVINE TRYPSIN
2btc 2BTC IS A RELATED INHIBITOR COMPLEXED WITH BOVINE TRYPSIN
2sta 2STA IS WILD TYPE SEQUENCE OF THE SAME PROTEIN COMPLEXED WITH SALMON TRYPSIN
2stb 2STB IS A RELATED INHIBITOR COMPLEXED WITH SALMON TRYPSIN
3cti 3CTI IS NMR STRUCTURE OF WILD TYPE SEQUENCE OF THE SAME PROTEIN