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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF SULFIDE:QUINONE OXIDOREDUCTASE SER126ALA VARIANT FROM ACIDITHIOBACILLUS FERROOXIDANS
 
Authors :  M. M. Cherney, Y. Zhang, M. N. G. James, J. H. Weiner
Date :  15 Jul 11  (Deposition) - 16 May 12  (Release) - 13 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Sulfide:Quinone Oxidoreductase, Ser126Ala Variant, Integral Monotopic Membrane Protein, Complex With Sulfide, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Cherney, Y. Zhang, M. N. James, J. H. Weiner
Structure-Activity Characterization Of Sulfide:Quinone Oxidoreductase Variants.
J. Struct. Biol. V. 178 319 2012
PubMed-ID: 22542586  |  Reference-DOI: 10.1016/J.JSB.2012.04.007

(-) Compounds

Molecule 1 - SULFIDE-QUINONE REDUCTASE, PUTATIVE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: AFE_1792
    Mutation: YES
    Organism Scientific: ACIDITHIOBACILLUS FERROOXIDANS
    Organism Taxid: 243159
    Strain: ATCC 23270 / DSM 14882 / NCIB 8455

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2H2S5Ligand/IonHYDROSULFURIC ACID
3LMT1Ligand/IonDODECYL-BETA-D-MALTOSIDE
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (4, 16)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2H2S10Ligand/IonHYDROSULFURIC ACID
3LMT2Ligand/IonDODECYL-BETA-D-MALTOSIDE
4SO42Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:7 , GLY A:8 , ALA A:9 , GLY A:10 , THR A:11 , GLY A:12 , SER A:34 , ALA A:35 , ASN A:36 , VAL A:42 , PRO A:43 , SER A:77 , ALA A:78 , ALA A:104 , THR A:105 , GLY A:106 , PRO A:107 , CYS A:160 , PRO A:163 , VAL A:267 , GLY A:301 , ILE A:302 , LYS A:320 , THR A:321 , GLY A:322 , ILE A:325 , VAL A:355 , PHE A:357 , LYS A:391 , H2S A:505 , HOH A:508 , HOH A:509 , HOH A:530 , HOH A:543 , HOH A:560 , HOH A:567 , HOH A:612 , HOH A:645 , HOH A:700 , HOH A:701 , HOH A:792 , HOH A:801BINDING SITE FOR RESIDUE FAD A 500
2AC2SOFTWAREGLY A:162 , MET A:169 , GLY A:205 , ASP A:206 , ILE A:210 , LEU A:211 , GLU A:217 , CYS A:356 , ALA A:358 , ALA A:365 , PHE A:367 , TYR A:383 , HOH A:518 , HOH A:562 , HOH A:620 , HOH A:672 , HOH A:738BINDING SITE FOR RESIDUE LMT A 501
3AC3SOFTWAREGLY A:162 , CYS A:356 , H2S A:504 , H2S A:505 , HOH A:706BINDING SITE FOR RESIDUE H2S A 502
4AC4SOFTWARELEU A:109 , ALA A:126 , CYS A:128 , THR A:129 , HIS A:132BINDING SITE FOR RESIDUE H2S A 503
5AC5SOFTWARECYS A:160 , H2S A:502 , H2S A:505BINDING SITE FOR RESIDUE H2S A 504
6AC6SOFTWARECYS A:356 , FAD A:500 , H2S A:502 , H2S A:504BINDING SITE FOR RESIDUE H2S A 505
7AC7SOFTWARELYS A:374 , PRO A:375 , ARG A:376BINDING SITE FOR RESIDUE H2S A 506
8AC8SOFTWAREMET A:-2 , HIS A:3 , HIS A:97 , HOH A:676BINDING SITE FOR RESIDUE SO4 A 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SY4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:370 -Pro A:371
2Lys A:374 -Pro A:375

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SY4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SY4)

(-) Exons   (0, 0)

(no "Exon" information available for 3SY4)

(-) 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:421
 aligned with SQRD_ACIF2 | B7JBP8 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:421
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                 
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417 
           SQRD_ACIF2     - ---MAHVVILGAGTGGMPAAYEMKEALGSGHEVTLISANDYFQFVPSNPWVGVGWKERDDIAFPIRHYVERKGIHFIAQSAEQIDAEAQNITLADGNTVHYDYLMIATGPKLAFENVPGSDPHEGPVQSICTVDHAERAFAEYQALLREPGPIVIGAMAGASCFGPAYEYAMIVASDLKKRGMRDKIPSFTFITSEPYIGHLGIQGVGDSKGILTKGLKEEGIEAYTNCKVTKVEDNKMYVTQVDEKGETIKEMVLPVKFGMMIPAFKGVPAVAGVEGLCNPGGFVLVDEHQRSKKYANIFAAGIAIAIPPVETTPVPTGAPKTGYMIESMVSAAVHNIKADLEGRKGEQTMGTWNAVCFADMGDRGAAFIALPQLKPRKVDVFAYGRWVHLAKVAFEKYFIRKMKMGVSEPFYEKVLFKM 418
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee....hhhhhhhhhhhhhh....eeee....eee...hhhhhhh...hhhhheeehhhhhhh...eee...eeeee....eeee....eee..eeee....ee.hhhh.........ee...hhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhh..hhhhh..eeeee..............hhhhhhhhhhhhh..eee..eeeeeee..eeeeeee.....eeeeeeee..eeeee..ee.hhhhhh........................eee.hhhh................hhhhhhhhhhhhhhhhhhhhh............eeeeee....eeeeeee.......eeeeeeehhhhhhhhhhhhhhhhhhhhh.......hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sy4 A  -2 MRGSAHVVILGAGTGGMPAAYEMKEALGSGHEVTLISANDYFQFVPSNPWVGVGWKERDDIAFPIRHYVERKGIHFIAQSAEQIDAEAQNITLADGNTVHYDYLMIATGPKLAFENVPGSDPHEGPVQAICTVDHAERAFAEYQALLREPGPIVIGAMAGASCFGPAYEYAMIVASDLKKRGMRDKIPSFTFITSEPYIGHLGIQGVGDSKGILTKGLKEEGIEAYTNCKVTKVEDNKMYVTQVDEKGETIKEMVLPVKFGMMIPAFKGVPAVAGVEGLCNPGGFVLVDEHQRSKKYANIFAAGIAIAIPPVETTPVPTGAPKTGYMIESMVSAAVHNIKADLEGRKGEQTMGTWNAVCFADMGDRGAAFIALPQLKPRKVDVFAYGRWVHLAKVAFEKYFIRKMKMGVSEPFYEKVLFKM 418
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417
   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 3SY4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SY4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SY4)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (SQRD_ACIF2 | B7JBP8)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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.
    GO:0048038    quinone binding    Interacting selectively and non-covalently with a quinone, any member of a class of diketones derivable from aromatic compounds by conversion of two CH groups into CO groups with any necessary rearrangement of double bonds.
biological process
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 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
    FAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    H2S  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    LMT  [ 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 ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:370 - Pro A:371   [ RasMol ]  
    Lys A:374 - Pro A:375   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  3sy4
    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
  SQRD_ACIF2 | B7JBP8
    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)
  (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
  SQRD_ACIF2 | B7JBP8
    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
        SQRD_ACIF2 | B7JBP8: 3kpk 3sx6 3sxi 3syi 3sz0 3szc 3szf 3szw 3t0k 3t14 3t2k 3t2y 3t2z 3t31

(-) Related Entries Specified in the PDB File

3kpg 3kpi 3kpk 3sx6 3sxi 3syi 3sz0 3szc 3szf