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 :  2.10
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
    Chains: A
    EC Number: 3.4.24.83
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG10
    Expression System Strain: ROSETTA 2 PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 298-809
    Gene: LEF, PXO1-107, BXA0172, GBAA_PXO1_0172
    Mutation: YES
    Organism Scientific: BACILLUS ANTHRACIS
    Organism Taxid: 1392
    Synonym: LF,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
156Q1Ligand/IonN~2~-[(4-FLUORO-3-METHYLPHENYL)SULFONYL]-N-HYDROXY-N~2~-METHYL-D-ALANINAMIDE
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:655 , LYS A:656 , GLY A:657 , GLY A:674 , VAL A:675 , LEU A:677 , HIS A:686 , GLU A:687 , HIS A:690 , TYR A:728 , GLU A:735 , GLU A:739 , ARG A:742 , ZN A:802 , HOH A:950binding site for residue 56Q A 801
2AC2SOFTWAREHIS A:686 , HIS A:690 , GLU A:735 , 56Q A:801binding site for residue ZN A 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D1S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5D1S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D1S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D1S)

(-) Exons   (0, 0)

(no "Exon" information available for 5D1S)

(-) 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:507
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhh.........hhhhhhhhhhhhhhhhh..hhhhhhhh......hhhhhhhhhhhhhhh...hhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...hhhhhh....eeeeehhhhhhhhhhhh..........hhhhhhhhhhhh.eeee....eee...........eeeeee......eeee...eeee...eeeeeeeeeeee....eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhh...hhhhh....eeee....eeeee.........hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d1s A 265 LSRYEKWEKIKQHYQHWSDSLSEEGRGLLKKLQIPIEPKKDDIIHSLSQEEKELLKRIQIDSSDFLSTEEKEFLKKLQIDIRDSLSEEEKELLNRINPLSEKEKEFLKKLKLDIQPYDINQRLQDTGGLIDSPSINLDVRKQYKRDIQNIDALLHQSIGSTLYNKIYLYENMNINNLTATLGADLVDSTDNTKINRGIFNEFKKNFKYSISSNYMIVDINERPALDNERLKWRIQLSPDTRAGYLENGKLILQRNIGLEIKDVQIIKQSEKEYIRIDAKVVPKSKIDTKIQEAQLNINQEWNKALGLPKYTKLITFNVHNRYASNIVESAYLILNEWKNNIQSDLIKKVTNYLVDGNGRFVFTDITLPNIAEQYTHQDEIYEQVHSKGLYVPESRSILLHGPSKGVELRNDSEGFIHEFGHAVDDYAGYLLDKNQSDLVTNSKKFIDIFKEEGSNLTSYGRTNEAEFFAEAFRLMHSTDHAERLKVQKNAPKTFQFINDQIKFIINS 776
                                   274       284       294       304       314       324       334       344       354     ||369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       
                                                                                                                         360|                                                                                                                                                                                                                                                                                                                                                                                                                          
                                                                                                                          366
   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 5D1S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D1S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D1S)

(-) 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
    56Q  [ 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 5d1s)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  5d1s
    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
  LEF_BACAN | P15917
    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)
  3.4.24.83
    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
  LEF_BACAN | P15917
    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
        LEF_BACAN | P15917: 1j7n 1jky 1pwp 1pwq 1pwu 1pwv 1pww 1yqy 1zxv 2l0r 3kwv 4dv8 4pkq 4pkr 4pks 4pkt 4pku 4pkv 4pkw 4wf6 4xm6 4xm7 4xm8 5d1t 5d1u

(-) 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