Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF BACILLUS SUBTILIS LON N-TERMINAL DOMAIN
 
Authors :  R. E. Duman, J. Y. Lowe
Date :  15 Mar 10  (Deposition) - 30 Jun 10  (Release) - 25 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Coiled-Coil, Atp-Binding, Hydrolase, Nucleotide-Binding, Protease, Serine Protease, Stress Response (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. E. Duman, J. Lowe
Crystal Structures Of Bacillus Subtilis Lon Protease.
J. Mol. Biol. V. 401 653 2010
PubMed-ID: 20600124  |  Reference-DOI: 10.1016/J.JMB.2010.06.030

(-) Compounds

Molecule 1 - ATP-DEPENDENT PROTEASE LA 1
    ChainsA, B
    EC Number3.4.21.53
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A+
    Expression System StrainBL21(AI)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentBSLON, N-TERMINAL DOMAIN
    GeneBSU28200, LON, LONA
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid224308
    Strain168

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3M65)

(-) Sites  (0, 0)

(no "Site" information available for 3M65)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M65)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:117 -Asp A:118

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M65)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LON_NPS51787 Lon N-terminal domain profile.LON1_BACSU9-200
 
  2A:9-200
B:9-200
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LON_NPS51787 Lon N-terminal domain profile.LON1_BACSU9-200
 
  1A:9-200
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LON_NPS51787 Lon N-terminal domain profile.LON1_BACSU9-200
 
  1-
B:9-200
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LON_NPS51787 Lon N-terminal domain profile.LON1_BACSU9-200
 
  2A:9-200
B:9-200

(-) Exons   (0, 0)

(no "Exon" information available for 3M65)

(-) 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:204
 aligned with LON1_BACSU | P37945 from UniProtKB/Swiss-Prot  Length:774

    Alignment length:206
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203      
           LON1_BACSU     4 ELKRSIPLLPLRGLLVYPTMVLHLDVGRDKSVQALEQAMMHDHMIFLATQQDISIDEPGEDEIFTVGTYTKIKQMLKLPNGTIRVLVEGLKRAHIVKYNEHEDYTSVDIQLIHEDDSKDTEDEALMRTLLDHFDQYIKISKKISAETYAAVTDIEEPGRMADIVASHLPLKLKDKQDILETADVKDRLNKVIDFINNEKEVLEIEK 209
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.........eeeeee.hhhhhhhhhhhh....eeeeee.........hhhhh..eeeeeeeeeeee.....eeeeeeeeeeeeeeeeee....eeeeeee....--..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----LON_N  PDB: A:9-200 UniProt: 9-200                                                                                                                                                              --------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m65 A   4 ELKRSIPLLPLRGLLVYPTMVLHLDVGRDKSVQALEQAMMHDHMIFLATQQDISIDEPGEDEIFTVGTYTKIKQMLKLPNGTIRVLVEGLKRAHIVKYNEHEDYTSVDIQLIHED--KDTEDEALMRTLLDHFDQYIKISKKISAETYAAVTDIEEPGRMADIVASHLPLKLKDKQDILETADVKDRLNKVIDFINNEKEVLEIEK 209
                                    13        23        33        43        53        63        73        83        93       103       113    |  123       133       143       153       163       173       183       193       203      
                                                                                                                                            118  |                                                                                        
                                                                                                                                               121                                                                                        

Chain B from PDB  Type:PROTEIN  Length:204
 aligned with LON1_BACSU | P37945 from UniProtKB/Swiss-Prot  Length:774

    Alignment length:206
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203      
           LON1_BACSU     4 ELKRSIPLLPLRGLLVYPTMVLHLDVGRDKSVQALEQAMMHDHMIFLATQQDISIDEPGEDEIFTVGTYTKIKQMLKLPNGTIRVLVEGLKRAHIVKYNEHEDYTSVDIQLIHEDDSKDTEDEALMRTLLDHFDQYIKISKKISAETYAAVTDIEEPGRMADIVASHLPLKLKDKQDILETADVKDRLNKVIDFINNEKEVLEIEK 209
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----LON-3m65B01 B:8-200                                                                                                                                                                              --------- Pfam domains (1)
           Pfam domains (2) ----LON-3m65B02 B:8-200                                                                                                                                                                              --------- Pfam domains (2)
         Sec.struct. author .eeeeeeeeee.........eeeeee.hhhhhhhhhhhh....eeeeee.........hhhhh..eeeeeeeeeeee.....eeeeeeeeeeeeeeeeee....eeeeeee....--..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----LON_N  PDB: B:9-200 UniProt: 9-200                                                                                                                                                              --------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m65 B   4 ELKRSIPLLPLRGLLVYPTMVLHLDVGRDKSVQALEQAMMHDHMIFLATQQDISIDEPGEDEIFTVGTYTKIKQMLKLPNGTIRVLVEGLKRAHIVKYNEHEDYTSVDIQLIHED--KDTEDEALMRTLLDHFDQYIKISKKISAETYAAVTDIEEPGRMADIVASHLPLKLKDKQDILETADVKDRLNKVIDFINNEKEVLEIEK 209
                                    13        23        33        43        53        63        73        83        93       103       113    |  123       133       143       153       163       173       183       193       203      
                                                                                                                                            118  |                                                                                        
                                                                                                                                               121                                                                                        

   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  (0, 0)

(no "SCOP Domain" information available for 3M65)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M65)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PUA (42)
(-)
Family: LON (3)
1aLON-3m65B01B:8-200
1bLON-3m65B02B:8-200

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (LON1_BACSU | P37945)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004176    ATP-dependent peptidase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the hydrolysis of peptide bonds.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    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:0033554    cellular response to stress    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
    GO:0006515    misfolded or incompletely synthesized protein catabolic process    The chemical reactions and pathways resulting in the breakdown of misfolded or attenuated proteins.
    GO:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
(no "Ligands, Modified Residues, Ions" information available for 3m65)
 
  Sites
(no "Sites" information available for 3m65)
 
  Cis Peptide Bonds
    Glu A:117 - Asp A:118   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3m65
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  LON1_BACSU | P37945
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.21.53
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  LON1_BACSU | P37945
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        LON1_BACSU | P379451x37 3m6a

(-) Related Entries Specified in the PDB File

3m6a