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 :  CRYSTAL STRUCTURE OF THIOREDOXIN-LIKE SUPERFAMILY PROTEIN SPOA0173
 
Authors :  C. Chang, N. Marshall, L. Freeman, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  21 Oct 08  (Deposition) - 04 Nov 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Thioredoxin-Like Superfamily Protein Spoa0173, Silicibacter Pomeroyi Dss, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, N. Marshall, L. Freeman, A. Joachimiak
Crystal Structure Of Thioredoxin-Like Superfamily Protein Spoa0173
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN SPOA0173
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21(DE3) DERIVATIVES
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SPOA0173
    Organism Scientific: SILICIBACTER POMEROYI
    Organism Taxid: 89184

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 34)

Asymmetric/Biological Unit (3, 34)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2EDO3Ligand/Ion1,2-ETHANEDIOL
3MSE28Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:8 , ASP A:17 , HOH A:337 , GLN D:9 , GLN D:97BINDING SITE FOR RESIDUE EDO A 201
2AC2SOFTWAREPRO A:98 , GLY A:99 , ASP A:100 , ARG A:105 , GLN D:10 , TRP D:11BINDING SITE FOR RESIDUE EDO A 203
3AC3SOFTWAREGLN A:49 , ARG A:52 , ARG A:88 , ILE A:89 , LYS A:90 , PHE A:91 , HOH A:319 , HOH A:367 , HOH A:443BINDING SITE FOR RESIDUE ACY A 202
4AC4SOFTWAREGLN B:49 , ARG B:88 , ILE B:89 , LYS B:90 , PHE B:91 , HOH B:219 , HOH B:311BINDING SITE FOR RESIDUE ACY B 201
5AC5SOFTWAREGLY C:99 , ASP C:100 , GLY C:101 , MSE C:103BINDING SITE FOR RESIDUE EDO C 201
6AC6SOFTWAREGLN D:49 , ARG D:52 , ARG D:88 , ILE D:89 , LYS D:90 , PHE D:91 , HOH D:221 , HOH D:278 , HOH D:333BINDING SITE FOR RESIDUE ACY D 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Thr A:115 -Pro A:116
2Thr B:115 -Pro B:116
3Thr C:115 -Pro C:116
4Thr D:115 -Pro D:116

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EYT)

(-) Exons   (0, 0)

(no "Exon" information available for 3EYT)

(-) 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:156
 aligned with Q5LL54_RUEPO | Q5LL54 from UniProtKB/TrEMBL  Length:175

    Alignment length:156
                               1                                                                                                                                                        
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147      
         Q5LL54_RUEPO     - ---MKAPELQIQQWFNSATDLTLADLRGKVIVIEAFQMLCPGCVMHGIPLAQKVRAAFPEDKVAVLGLHTVFEHHEAMTPISLKAFLHEYRIKFPVGVDQPGDGAMPRTMAAYQMRGTPSLLLIDKAGDLRAHHFGDVSELLLGAEIATLLGEAAP 153
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3eytA00 A:-2-153 Glutaredoxin                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee.....eeeee.......hhhhh..eeeeeee...hhhhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhh.....eeee.......hhhhhhh......eeeee....eeeeeee...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3eyt A  -2 SNAmKAPELQIQQWFNSATDLTLADLRGKVIVIEAFQmLCPGCVmHGIPLAQKVRAAFPEDKVAVLGLHTVFEHHEAmTPISLKAFLHEYRIKFPVGVDQPGDGAmPRTmAAYQmRGTPSLLLIDKAGDLRAHHFGDVSELLLGAEIATLLGEAAP 153
                               |     7        17        27       |37    |   47        57        67       |77        87        97     | 107    |  117       127       137       147      
                               |                                35-MSE 42-MSE                           75-MSE                     103-MSE    |                                         
                               1-MSE                                                                                                   107-MSE|                                         
                                                                                                                                            112-MSE                                     


Chain B from PDB  Type:PROTEIN  Length:154
 aligned with Q5LL54_RUEPO | Q5LL54 from UniProtKB/TrEMBL  Length:175

    Alignment length:154
                             1                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149    
         Q5LL54_RUEPO     - -MKAPELQIQQWFNSATDLTLADLRGKVIVIEAFQMLCPGCVMHGIPLAQKVRAAFPEDKVAVLGLHTVFEHHEAMTPISLKAFLHEYRIKFPVGVDQPGDGAMPRTMAAYQMRGTPSLLLIDKAGDLRAHHFGDVSELLLGAEIATLLGEAAP 153
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3eytB00 B:0-153 Glutaredoxin                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.......hhhhh..eeeeeee...hhhhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhh.....eeee.......hhhhhhhh.....eeeee.....eeeeee...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eyt B   0 AmKAPELQIQQWFNSATDLTLADLRGKVIVIEAFQmLCPGCVmHGIPLAQKVRAAFPEDKVAVLGLHTVFEHHEAmTPISLKAFLHEYRIKFPVGVDQPGDGAmPRTmAAYQmRGTPSLLLIDKAGDLRAHHFGDVSELLLGAEIATLLGEAAP 153
                             |       9        19        29     |  39  |     49        59        69     |  79        89        99   |   109  |    119       129       139       149    
                             1-MSE                            35-MSE 42-MSE                           75-MSE                     103-MSE    |                                         
                                                                                                                                     107-MSE|                                         
                                                                                                                                          112-MSE                                     


Chain C from PDB  Type:PROTEIN  Length:157
 aligned with Q5LL54_RUEPO | Q5LL54 from UniProtKB/TrEMBL  Length:175

    Alignment length:157
                               1                                                                                                                                                         
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       
         Q5LL54_RUEPO     - ---MKAPELQIQQWFNSATDLTLADLRGKVIVIEAFQMLCPGCVMHGIPLAQKVRAAFPEDKVAVLGLHTVFEHHEAMTPISLKAFLHEYRIKFPVGVDQPGDGAMPRTMAAYQMRGTPSLLLIDKAGDLRAHHFGDVSELLLGAEIATLLGEAAPS 154
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3eytC00 C:-2-154 Glutaredoxin                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.....eeeee.......hhhhh..eeeeeee...hhhhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhh.....eeee.......hhhhhhh......eeeee....eeeeeee...hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eyt C  -2 SNAmKAPELQIQQWFNSATDLTLADLRGKVIVIEAFQmLCPGCVmHGIPLAQKVRAAFPEDKVAVLGLHTVFEHHEAmTPISLKAFLHEYRIKFPVGVDQPGDGAmPRTmAAYQmRGTPSLLLIDKAGDLRAHHFGDVSELLLGAEIATLLGEAAPS 154
                               |     7        17        27       |37    |   47        57        67       |77        87        97     | 107    |  117       127       137       147       
                               1-MSE                            35-MSE 42-MSE                           75-MSE                     103-MSE    |                                          
                                                                                                                                       107-MSE|                                          
                                                                                                                                            112-MSE                                      


Chain D from PDB  Type:PROTEIN  Length:155
 aligned with Q5LL54_RUEPO | Q5LL54 from UniProtKB/TrEMBL  Length:175

    Alignment length:155
                               1                                                                                                                                                       
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147     
         Q5LL54_RUEPO     - ---MKAPELQIQQWFNSATDLTLADLRGKVIVIEAFQMLCPGCVMHGIPLAQKVRAAFPEDKVAVLGLHTVFEHHEAMTPISLKAFLHEYRIKFPVGVDQPGDGAMPRTMAAYQMRGTPSLLLIDKAGDLRAHHFGDVSELLLGAEIATLLGEAA 152
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3eytD00 D:-2-152 Glutaredoxin                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee.......hhhhh..eeeeeee...hhhhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhh.....eeee.......hhhhhhh......eeeee.....eeeeee...hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eyt D  -2 SNAmKAPELQIQQWFNSATDLTLADLRGKVIVIEAFQmLCPGCVmHGIPLAQKVRAAFPEDKVAVLGLHTVFEHHEAmTPISLKAFLHEYRIKFPVGVDQPGDGAmPRTmAAYQmRGTPSLLLIDKAGDLRAHHFGDVSELLLGAEIATLLGEAA 152
                               |     7        17        27       |37    |   47        57        67       |77        87        97     | 107    |  117       127       137       147     
                               1-MSE                            35-MSE 42-MSE                           75-MSE                     103-MSE    |                                        
                                                                                                                                       107-MSE|                                        
                                                                                                                                            112-MSE
   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 3EYT)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EYT)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q5LL54_RUEPO | Q5LL54)
molecular function
    GO:0016209    antioxidant activity    Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

 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
    ACY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ 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 ]
 
  Cis Peptide Bonds
    Thr A:115 - Pro A:116   [ RasMol ]  
    Thr B:115 - Pro B:116   [ RasMol ]  
    Thr C:115 - Pro C:116   [ RasMol ]  
    Thr D:115 - Pro D:116   [ RasMol ]  
 

(-) 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
  3eyt
    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
  Q5LL54_RUEPO | Q5LL54
    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)
  (no 'Enzyme Classificator' available)
    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
  Q5LL54_RUEPO | Q5LL54
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3EYT)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3EYT)