Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
(-)Biological Unit 5
collapse expand < >
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)
Image Biological Unit 5
Biological Unit 5  (Jmol Viewer)

(-) Description

Title :  THE ANTIMICROBIAL PEPTIDASE LYSOSTAPHIN FROM STAPHYLOCOCCUS SIMULANS
 
Authors :  I. Sabala, E. Jagielska, P. T. Bardelang, H. Czapinska, S. O. Dahms, J. A R. James, M. E. Than, N. R. Thomas, M. Bochtler
Date :  29 Jul 13  (Deposition) - 09 Jul 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Peptidase Family M23, Peptidoglycan Hydrolase, Metallopeptidase, Peptidoglycan, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Sabala, E. Jagielska, P. T. Bardelang, H. Czapinska, S. O. Dahms, J. A. Sharpe, R. James, M. E. Than, N. R. Thomas, M. Bochtler
Crystal Structure Of The Antimicrobial Peptidase Lysostaphi From Staphylococcus Simulans.
Febs J. V. 281 4112 2014
PubMed-ID: 25039253  |  Reference-DOI: 10.1111/FEBS.12929

(-) Compounds

Molecule 1 - LYSOSTAPHIN
    Chains: A, B, C, D
    EC Number: 3.4.24.75
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 248-493
    Gene: LSS, U66883.1
    Organism Scientific: STAPHYLOCOCCUS SIMULANS
    Organism Taxid: 1286
    Strain: STAPHYLOCOCCUS SIMULANS BV. STAPHYLOLYTICUS
    Synonym: GLYCYL-GLYCINE ENDOPEPTIDASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (1x): A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1SO49Ligand/IonSULFATE ION
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 5 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:279 , ASP A:283 , HIS A:362 , SO4 A:602BINDING SITE FOR RESIDUE ZN A 601
02AC2SOFTWARETYR A:270 , ILE A:274 , HIS A:279 , ASP A:283 , HIS A:329 , HIS A:360 , HIS A:362 , ZN A:601BINDING SITE FOR RESIDUE SO4 A 602
03AC3SOFTWAREASN A:405 , LYS A:406BINDING SITE FOR RESIDUE SO4 A 603
04AC4SOFTWAREHIS B:279 , ASP B:283 , HIS B:362BINDING SITE FOR RESIDUE ZN B 601
05AC5SOFTWAREASN B:405 , LYS B:406BINDING SITE FOR RESIDUE SO4 B 602
06AC6SOFTWARESER B:371 , ASN B:372 , SER B:373BINDING SITE FOR RESIDUE SO4 B 603
07AC7SOFTWARETRP B:402 , LYS B:454BINDING SITE FOR RESIDUE SO4 B 604
08AC8SOFTWAREHIS C:279 , ASP C:283 , HIS C:362BINDING SITE FOR RESIDUE ZN C 601
09AC9SOFTWAREHIS D:279 , ASP D:283 , HIS D:362BINDING SITE FOR RESIDUE ZN D 601
10BC1SOFTWAREHIS D:323 , ARG D:365 , ASN D:368BINDING SITE FOR RESIDUE SO4 D 602
11BC2SOFTWAREARG C:427 , ARG C:433 , ALA D:249 , THR D:393BINDING SITE FOR RESIDUE SO4 D 603
12BC3SOFTWAREGLN D:256 , ASN D:259 , LYS D:389BINDING SITE FOR RESIDUE SO4 D 604
13BC4SOFTWAREASN D:405 , LYS D:406BINDING SITE FOR RESIDUE SO4 D 605

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LXC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4LXC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LXC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LXC)

(-) Exons   (0, 0)

(no "Exon" information available for 4LXC)

(-) 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:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhh......ee........ee..eeee.....eee....eeeeeeeee....eeeeeeee....eeeeee.eeee......ee....eeeee.........eeeeeeee..........hhhhhhhh...ee............ee.....eeeeeeeeeee...eeee.........eeeee.....eeeeeeeee..eeeeeee.....eeeeeeeeee....ee....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lxc A 248 AATHEHSAQWLNNYKKGYGYGPYPLGINGGMHYGVDFFMNIGTPVKAISSGKIVEAGWSNYGGGNQIGLIENDGVHRQWYMHLSKYNVKVGDYVKAGQIIGWSGSTGYSTAPHLHFQRMVNSFSNSTAQDPMPFLKSAGYGKAGGTVTPTPNTGWKTNKYGTLYKSESASFTPNTDIITRTTGPFRSMPQSGVLKAGQTIHYDEVMKQDGHVWVGYTGNSGQRIYLPVRTWNKSTNTLGVLWGTIK 493
                                   257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487      


Chain B from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhh......ee........ee..eeee.....eee....eeeeeeeee....eeeeeeee.....eeeee.eeee......ee....eeeee.........eeeeeee........ee.hhhhhhhh.................ee.....eeeeeeeeeee..eeeee.........eeeee.....eeeeeeeee..eeeeeee.....eeeeeeee............eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lxc B 254 SAQWLNNYKKGYGYGPYPLGINGGMHYGVDFFMNIGTPVKAISSGKIVEAGWSNYGGGNQIGLIENDGVHRQWYMHLSKYNVKVGDYVKAGQIIGWSGSTGYSTAPHLHFQRMVNSFSNSTAQDPMPFLKSAGYGKAGGTVTPTPNTGWKTNKYGTLYKSESASFTPNTDIITRTTGPFRSMPQSGVLKAGQTIHYDEVMKQDGHVWVGYTGNSGQRIYLPVRTWNKSTNTLGVLWGTIK 493
                                   263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493


Chain C from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhh.ee.............eeee.....eee....eeeeeeeee....eeeeeeee....eeeeeeeeeee......ee....eeeee.........eeee..ee..........hhhhhhhhh................ee.....eeeeeeeeeee...eeee.........eeeee.....eeeeeeeee..eeeeeee.....eeeeeeee............eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lxc C 249 ATHEHSAQWLNNYKKGYGYGPYPLMHYGVDFFMNIGTPVKAISSGKIVEAGWSNYGGGNQIGLIENDGVHRQWYMHLSKYNVKVGDYVKAGQIIGWSGSTGYSTAPHLHFQRMVNSFSNSTAQDPMPFLKSAGYGKAGGTVTPTPNTGWKTNKYGTLYKSESASFTPNTDIITRTTGPFRSMPQSGVLKAGQTIHYDEVMKQDGHVWVGYTGNSGQRIYLPVRTWNKSTNTLGVLWGTIK 493
                                   258       268   ||  283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493
                                                 272|                                                                                                                                                                                                                       
                                                  278                                                                                                                                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhh......ee........ee..eeee.....eee....eeeeeeeee....eeeeeeee....eeeeeeeeeee......ee....eeeee.........eeeeeeee.......ee.hhhhhhhhh................ee.....eeeeeeeeeee...eeeee........eeeee.....eeeeeeeee..eeeeeee.....eeeeeeee............eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lxc D 249 ATHEHSAQWLNNYKKGYGYGPYPLGINGGMHYGVDFFMNIGTPVKAISSGKIVEAGWSNYGGGNQIGLIENDGVHRQWYMHLSKYNVKVGDYVKAGQIIGWSGSTGYSTAPHLHFQRMVNSFSNSTAQDPMPFLKSAGYGKAGGTVTPTPNTGWKTNKYGTLYKSESASFTPNTDIITRTTGPFRSMPQSGVLKAGQTIHYDEVMKQDGHVWVGYTGNSGQRIYLPVRTWNKSTNTLGVLWGTIKL 494
                                   258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488
   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 4LXC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LXC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LXC)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

 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
    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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4lxc)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ 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 | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 PNG format | Biol. Unit 5 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
  4lxc
    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
  LSTP_STASI | P10547
    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)
  3.4.24.75
    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
  LSTP_STASI | P10547
    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
        LSTP_STASI | P10547: 4qp5 4qpb 5leo

(-) Related Entries Specified in the PDB File

1qwy LATENT LYTM AT 1.3 A RESOLUTION
1r77 CRYSTAL STRUCTURE OF THE CELL WALL TARGETING DOMAIN OF PEPTIDYLGLYCAN HYDROLASE ALE-1
2b0p TRUNCATED S. AUREUS LYTM, P212121 CRYSTAL FORM
2b13 TRUNCATED S. AUREUS LYTM, P41 CRYSTAL FORM
2b44 TRUNCATED S. AUREUS LYTM, P 32 2 1 CRYSTAL FORM
3it5 CRYSTAL STRUCTURE OF THE LASA VIRULENCE FACTOR FROM PSEUDOMONAS AERUGINOSA
3it7 CRYSTAL STRUCTURE OF THE LASA VIRULENCE FACTOR FROM PSEUDOMONAS AERUGINOSA
4bh5 LYTM DOMAIN OF ENVC, AN ACTIVATOR OF CELL WALL AMIDASES IN ESCHERICHIA COLI
4qp5
4qpb