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 :  ANTHRAX TOXIN LETHAL FACTOR WITH HYDROXAMIC ACID INHIBITOR
 
Authors :  K. M. Maize, B. C. Finzel
Date :  04 Aug 15  (Deposition) - 11 Nov 15  (Release) - 25 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Anthrax Toxin, Lethal Factor, Metalloproteinase, Metalloprotease, Structural Dynamics, Ligand-Induced Conformational Change, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. K. Kurbanov, T. L. Chiu, J. Solberg, S. Francis, K. M. Maize, J. Fernandez, R. L. Johnson, J. E. Hawkinson, M. A. Walters, B. C. Finzel, E. A. Amin
Probing The S2' Subsite Of The Anthrax Toxin Lethal Factor Using Novel N-Alkylated Hydroxamates.
J. Med. Chem. V. 58 8723 2015
PubMed-ID: 26492514  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01446

(-) Compounds

Molecule 1 - LETHAL FACTOR
    ChainsA
    EC Number3.4.24.83
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG10
    Expression System StrainROSETTA 2 PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 298-809
    GeneLEF, PXO1-107, BXA0172, GBAA_PXO1_0172
    MutationYES
    Organism ScientificBACILLUS ANTHRACIS
    Organism Taxid1392
    SynonymLF,ANTHRAX LETHAL TOXIN ENDOPEPTIDASE COMPONENT

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
156P1Ligand/IonN~2~-(6-AMINOHEXYL)-N~2~-[(4-FLUORO-3-METHYLPHENYL)SULFONYL]-N-HYDROXY-D-ALANINAMIDE
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:655 , LYS A:656 , GLY A:657 , VAL A:675 , LEU A:677 , HIS A:686 , GLU A:687 , HIS A:690 , TYR A:728 , GLU A:735 , GLU A:739 , ZN A:802binding site for residue 56P A 801
2AC2SOFTWAREHIS A:686 , HIS A:690 , GLU A:735 , 56P A:801binding site for residue ZN A 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D1U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5D1U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D1U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D1U)

(-) Exons   (0, 0)

(no "Exon" information available for 5D1U)

(-) 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:488
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhh..hhhhhhhhhh.........hhhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.............eeeeehhhhhhhhhhh...........hhhhhhhhh....eeee....eee...........eeeeee......eeee...eeee...eeeeeeeeeeee....eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhh...hhhhh....eeeehhh.eeeee.........hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d1u A 267 RYEKWEKIKQHYQHWSDSLSEEGRGLLKKLQIPIEPKKDDIIHSLSQEEKELLKRIQIDSSDFLSTEEKEFLKKLQIDILSEKEKEFLKKLKLDIQPYDINQRLQDTGGLIDSPSINLDVRKQYKRDIQNIDALLHQSIGSTLYNKIYLYENMNINNLTATLGADLVDSTDNTKINRGIFNEFKKNFKYSISSNYMIVDINERPALDNERLKWRIQLSPDTRAGYLENGKLILQRNIGLEIKDVQIIKQSEKEYIRIDAKVVPKSKIDTKIQEAQLNINQEWNKALGLPKYTKLITFNVHNRYASNIVESAYLILNEWKNNIQSDLIKKVTNYLVDGNGRFVFTDITLPNIAEQYTHQDEIYEQVHSKGLYVPESRSILLHGPSKGVELRNDSEGFIHEFGHAVDDYAGYLLDKNQSDLVTNSKKFIDIFKEEGSNLTSYGRTNEAEFFAEAFRLMHSTDHAERLKVQKNAPKTFQFINDQIKFIINS 776
                                   276       286       296       306       316       326       336       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768        
                                                                                                        345|                                                                                                                                                                                                                                                                                                                                                                                                                        
                                                                                                         368                                                                                                                                                                                                                                                                                                                                                                                                                        

   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 5D1U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D1U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D1U)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    56P  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5d1u)
 

(-) 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
  5d1u
    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
  LEF_BACAN | P15917
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.24.83
    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
  LEF_BACAN | P15917
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        LEF_BACAN | P159171j7n 1jky 1pwp 1pwq 1pwu 1pwv 1pww 1yqy 1zxv 2l0r 3kwv 4dv8 4pkq 4pkr 4pks 4pkt 4pku 4pkv 4pkw 4wf6 4xm6 4xm7 4xm8 5d1s 5d1t

(-) Related Entries Specified in the PDB File

1yqy THE N-TERMINALLY TRUNCATED PROTEIN COMPLEXED WITH A SMALL MOLECULE INHIBITOR IN A P212121 SPACEGROUP
4pkq THE N-TERMINALLY TRUNCATED PROTEIN IN A P212121 SPACEGROUP
4pkr THE N-TERMINALLY TRUNCATED PROTEIN COMPLEXED WITH A SMALL MOLECULE INHIBITOR IN A P212121 SPACEGROUP
4pks THE N-TERMINALLY TRUNCATED PROTEIN COMPLEXED WITH A SMALL MOLECULE INHIBITOR IN A P212121 SPACEGROUP
4pkt THE N-TERMINALLY TRUNCATED PROTEIN COMPLEXED WITH A SMALL MOLECULE INHIBITOR IN A P212121 SPACEGROUP
4pku THE N-TERMINALLY TRUNCATED PROTEIN COMPLEXED WITH A SMALL MOLECULE INHIBITOR IN A P212121 SPACEGROUP
4pkv THE N-TERMINALLY TRUNCATED PROTEIN COMPLEXED WITH A SMALL MOLECULE INHIBITOR IN A P212121 SPACEGROUP
4pkw THE N-TERMINALLY TRUNCATED PROTEIN COMPLEXED WITH GM6001 IN A P212121 SPACEGROUP