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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF METHIONINE SULFOXIDE REDUCTASE U16S FROM CLOSTRIDIUM OREMLANDII
 
Authors :  K. Y. Hwang, E. H. Lee
Date :  27 Jul 13  (Deposition) - 11 Jun 14  (Release) - 11 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha/Beta Fold, Peptide-Methionine (S)-S-Oxide Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. H. Lee, G. H. Kwak, M. J. Kim, H. Y. Kim, K. Y. Hwang
Structural Analysis Of 1-Cys Type Selenoprotein Methionine Sulfoxide Reductase A
Arch. Biochem. Biophys. V. 545 1 2014
PubMed-ID: 24412203  |  Reference-DOI: 10.1016/J.ABB.2013.12.024

(-) Compounds

Molecule 1 - PEPTIDE METHIONINE SULFOXIDE REDUCTASE MSRA
    Chains: A, B
    EC Number: 1.8.4.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3) STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MSRA
    Mutation: YES
    Organism Scientific: ALKALIPHILUS OREMLANDII
    Organism Taxid: 350688
    Strain: OHILAS
    Synonym: PROTEIN-METHIONINE-S-OXIDE REDUCTASE, PEPTIDE-METHIONINE (S)-S-OXIDE REDUCTASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:19 , ALA A:22 , GLN A:23 , THR A:42 , ASN A:43 , TYR A:141 , ASN A:178 , HOH A:473 , HOH A:556BINDING SITE FOR RESIDUE ACT A 301
2AC2SOFTWARETYR A:156 , SER A:165 , THR A:166 , LEU A:167 , HOH A:488 , HOH A:540 , HOH A:569BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREGLY B:19 , ALA B:22 , GLN B:23 , THR B:42 , ASN B:43 , TYR B:141 , ASN B:178 , HOH B:496BINDING SITE FOR RESIDUE ACT B 301
4AC4SOFTWARETYR B:156 , SER B:165 , THR B:166 , LEU B:167 , HOH B:500 , HOH B:533 , HOH B:555BINDING SITE FOR RESIDUE SO4 B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LWK)

(-) 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:205
                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhhhhh....eeeeeeeee...............eeeeeeee.....hhhhhhhhhhhhh.......hhhh.eeeee.hhhhhhhhhhhhhhhhhhhh.....eeee...eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lwk A   6 KLSIAVFALGSFWGPDAQFGSIKGVVSTRVGYAGGTTNNPSYYNLGDHSESIEIQYDANVITYGELLNIFWNLHNPVYETTNRQYMSRIFYLDDGQKSEALEMKRQIEAANGEKIYTEIVPLENFYLAEGYHQKYYLQNTTKLYQTLKAIYGGFGNLVRSTLAARMNGYIAGNLSIASLKEEMDLVELPEDQYEKVLSIVEEIKL 210
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205     


Chain B from PDB  Type:PROTEIN  Length:205
                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhhhhh....eeeeeeeee...............eeeeeeee.....hhhhhhhhhhhhh.......hhhh.eeeee.hhhhhhhhhhhhhhhhhhhh.....eeee...eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lwk B   6 KLSIAVFALGSFWGPDAQFGSIKGVVSTRVGYAGGTTNNPSYYNLGDHSESIEIQYDANVITYGELLNIFWNLHNPVYETTNRQYMSRIFYLDDGQKSEALEMKRQIEAANGEKIYTEIVPLENFYLAEGYHQKYYLQNTTKLYQTLKAIYGGFGNLVRSTLAARMNGYIAGNLSIASLKEEMDLVELPEDQYEKVLSIVEEIKL 210
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205
   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 4LWK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4lwk)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 ](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
  4lwk
    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
  A8MI53_ALKOO | A8MI53
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  1.8.4.11
    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
  A8MI53_ALKOO | A8MI53
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A8MI53_ALKOO | A8MI53: 4lwj 4lwl 4lwm 4u66 4w8c

(-) Related Entries Specified in the PDB File

4lwj 4lwl 4lwm 4lwn