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 :  PYRIDINE NUCLEOTIDE COMPLEXES WITH BACILLUS ANTHRACIS COENZYME A-DISULFIDE REDUCTASE: A STRUCTURAL ANALYSIS OF DUAL NAD(P)H SPECIFICITY
 
Authors :  J. R. Wallen
Date :  05 Mar 08  (Deposition) - 22 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Coenzyme A, Flavin Adenine Dinucleotide, Selenomethionine, Fad, Flavoprotein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Wallen, C. Paige, T. C. Mallett, P. A. Karplus, A. Claiborne
Pyridine Nucleotide Complexes With Bacillus Anthracis Coenzyme A-Disulfide Reductase: A Structural Analysis Of Dual Nad(P)H Specificity.
Biochemistry V. 47 5182 2008
PubMed-ID: 18399646  |  Reference-DOI: 10.1021/BI8002204

(-) Compounds

Molecule 1 - PYRIDINE NUCLEOTIDE-DISULFIDE OXIDOREDUCTASE, CLASS I
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRCHISC
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PYRIDINE NUCLEOTIDE-DISULFIDE OXIDOREDUCTASE, CLASS I
    Organism Scientific: BACILLUS ANTHRACIS STR.
    Organism Taxid: 198094
    Strain: AMES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 30)

Asymmetric/Biological Unit (3, 30)
No.NameCountTypeFull Name
1COA2Ligand/IonCOENZYME A
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3MSE26Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:9 , SER A:14 , GLN A:18 , ARG A:21 , SER A:38 , TYR A:39 , CYS A:42 , ARG A:61 , ASN A:304 , ARG A:308 , ARG B:441 , ARG B:442BINDING SITE FOR RESIDUE COA A 445
2AC2SOFTWAREARG A:441 , ARG A:442 , ASP B:9 , ALA B:10 , GLN B:18 , ARG B:21 , SER B:38 , TYR B:39 , CYS B:42 , ARG B:61 , ASN B:304 , ARG B:308BINDING SITE FOR RESIDUE COA B 445
3AC3SOFTWAREILE A:6 , GLY A:7 , ASP A:9 , ALA A:10 , ALA A:11 , LEU A:31 , GLU A:32 , LYS A:33 , GLN A:41 , CYS A:42 , HIS A:78 , ALA A:111 , THR A:112 , GLY A:113 , ILE A:161 , GLY A:281 , ASP A:282 , ILE A:299 , GLY A:300 , THR A:301 , ALA A:303 , TYR B:425 , ALA B:426 , PRO B:427BINDING SITE FOR RESIDUE FAD A 446
4AC4SOFTWARETYR A:425 , ALA A:426 , PRO A:427 , ILE B:6 , GLY B:7 , ASP B:9 , ALA B:10 , ALA B:11 , LEU B:31 , GLU B:32 , LYS B:33 , GLN B:41 , CYS B:42 , HIS B:78 , GLU B:79 , ALA B:111 , THR B:112 , GLY B:113 , ILE B:161 , GLY B:281 , ASP B:282 , ILE B:299 , GLY B:300 , THR B:301 , ALA B:303BINDING SITE FOR RESIDUE FAD B 446

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CGB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CGB)

(-) 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:444
 aligned with Q81TK8_BACAN | Q81TK8 from UniProtKB/TrEMBL  Length:444

    Alignment length:444
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440    
         Q81TK8_BACAN     1 MNYVIIGGDAAGMSAAMQIVRNDENANVVTLEKGEIYSYAQCGLPYVISGAIASTEKLIARNVKTFRDKYGIDAKVRHEVTKVDTEKKIVYAEHTKTKDVFEFSYDRLLIATGVRPVMPEWEGRDLQGVHLLKTIPDAERILKTLETNKVEDVTIIGGGAIGLEMAETFVELGKKVRMIERNDHIGTIYDGDMAEYIYKEADKHHIEILTNENVKAFKGNERVEAVETDKGTYKADLVLVSVGVKPNTDFLEGTNIRTNHKGAIEVNAYMQTNVQDVYAAGDCATHYHVIKEIHDHIPIGTTANKQGRLAGLNMLDKRRAFKGTLGTGIIKFMNLTLARTGLNEKEAKGLHIPYKTVKVDSTNMAGYYPNAKPLYLKLLYRSDTKQLLGGQVIGEEGVDKRIDVIAMALFNKMSIHDLEDVDLSYAPPYNSVWDPIQQAARRAE 444
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh...eeeee........hhhhhhhhhh....hhhhhh..hhhhhhhh...eee..eeeeeee....eeeeee.....eeeee..eeee...eee............ee...hhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhh..eeeee.hhhhh....hhhhhhhhhhhhhhh..eee....eeeeee...eeeeee..eeee..eeee...eee.hhhhh........................eee.hhhh.ee......ee...hhhhhhhhhhhhhhhhh............eeeee..eeeeeee.hhhhhhhh...eeeeeeeee..........eeeeeeeee.....eeeeeeee..hhhhhhhhhhhhhhh..hhhhhhhh............hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cgb A   1 mNYVIIGGDAAGmSAAmQIVRNDENANVVTLEKGEIYSYAQCGLPYVISGAIASTEKLIARNVKTFRDKYGIDAKVRHEVTKVDTEKKIVYAEHTKTKDVFEFSYDRLLIATGVRPVmPEWEGRDLQGVHLLKTIPDAERILKTLETNKVEDVTIIGGGAIGLEmAETFVELGKKVRmIERNDHIGTIYDGDmAEYIYKEADKHHIEILTNENVKAFKGNERVEAVETDKGTYKADLVLVSVGVKPNTDFLEGTNIRTNHKGAIEVNAYmQTNVQDVYAAGDCATHYHVIKEIHDHIPIGTTANKQGRLAGLNmLDKRRAFKGTLGTGIIKFmNLTLARTGLNEKEAKGLHIPYKTVKVDSTNmAGYYPNAKPLYLKLLYRSDTKQLLGGQVIGEEGVDKRIDVIAmALFNKmSIHDLEDVDLSYAPPYNSVWDPIQQAARRAE 444
                            |       10  |   | 20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    |  170       180       190  |    200       210       220       230       240       250       260       270       280       290       300       310   |   320       330  |    340       350       360   |   370       380       390       400      |410  |    420       430       440    
                            |          13-MSE                                                                                                  118-MSE                                        165-MSE      178-MSE        193-MSE                                                                      270-MSE                                     314-MSE            333-MSE                        364-MSE                                    407-MSE |                               
                            1-MSE          17-MSE                                                                                                                                                                                                                                                                                                                                                                                                     413-MSE                           


Chain B from PDB  Type:PROTEIN  Length:444
 aligned with Q81TK8_BACAN | Q81TK8 from UniProtKB/TrEMBL  Length:444

    Alignment length:444
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440    
         Q81TK8_BACAN     1 MNYVIIGGDAAGMSAAMQIVRNDENANVVTLEKGEIYSYAQCGLPYVISGAIASTEKLIARNVKTFRDKYGIDAKVRHEVTKVDTEKKIVYAEHTKTKDVFEFSYDRLLIATGVRPVMPEWEGRDLQGVHLLKTIPDAERILKTLETNKVEDVTIIGGGAIGLEMAETFVELGKKVRMIERNDHIGTIYDGDMAEYIYKEADKHHIEILTNENVKAFKGNERVEAVETDKGTYKADLVLVSVGVKPNTDFLEGTNIRTNHKGAIEVNAYMQTNVQDVYAAGDCATHYHVIKEIHDHIPIGTTANKQGRLAGLNMLDKRRAFKGTLGTGIIKFMNLTLARTGLNEKEAKGLHIPYKTVKVDSTNMAGYYPNAKPLYLKLLYRSDTKQLLGGQVIGEEGVDKRIDVIAMALFNKMSIHDLEDVDLSYAPPYNSVWDPIQQAARRAE 444
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh...eeeee........hhhhhhhhhh....hhhhhh..hhhhhhhh...eee..eeeeeee....eeeeee.....eeeee..eeee...eee............ee...hhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh..eeeee.hhhhh....hhhhhhhhhhhhhhh..eee....eeeee......eeee..eeee..eeee...eee.hhhhh........................eee.hhhh.ee......ee...hhhhhhhhhhhhhhhhh............eeeee..eeeeeee.hhhhhhhhh..eeeeeeeee..........eeeeeeeee.....eeeeeeee..hhhhhhhhhhhhhhh..hhhhhhhh............hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cgb B   1 mNYVIIGGDAAGmSAAmQIVRNDENANVVTLEKGEIYSYAQCGLPYVISGAIASTEKLIARNVKTFRDKYGIDAKVRHEVTKVDTEKKIVYAEHTKTKDVFEFSYDRLLIATGVRPVmPEWEGRDLQGVHLLKTIPDAERILKTLETNKVEDVTIIGGGAIGLEmAETFVELGKKVRmIERNDHIGTIYDGDmAEYIYKEADKHHIEILTNENVKAFKGNERVEAVETDKGTYKADLVLVSVGVKPNTDFLEGTNIRTNHKGAIEVNAYmQTNVQDVYAAGDCATHYHVIKEIHDHIPIGTTANKQGRLAGLNmLDKRRAFKGTLGTGIIKFmNLTLARTGLNEKEAKGLHIPYKTVKVDSTNmAGYYPNAKPLYLKLLYRSDTKQLLGGQVIGEEGVDKRIDVIAmALFNKmSIHDLEDVDLSYAPPYNSVWDPIQQAARRAE 444
                            |       10  |   | 20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    |  170       180       190  |    200       210       220       230       240       250       260       270       280       290       300       310   |   320       330  |    340       350       360   |   370       380       390       400      |410  |    420       430       440    
                            1-MSE      13-MSE                                                                                                  118-MSE                                        165-MSE      178-MSE        193-MSE                                                                      270-MSE                                     314-MSE            333-MSE                        364-MSE                                    407-MSE |                               
                                           17-MSE                                                                                                                                                                                                                                                                                                                                                                                                     413-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 3CGB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q81TK8_BACAN | Q81TK8)
molecular function
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    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:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

 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
    COA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FAD  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3cgb)
 

(-) 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
  3cgb
    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
  Q81TK8_BACAN | Q81TK8
    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
  Q81TK8_BACAN | Q81TK8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q81TK8_BACAN | Q81TK8: 3cgc 3cgd 3cge

(-) Related Entries Specified in the PDB File

3cgc THE SAME PROTEIN OXIDIZED
3cgd THE SAME PROTEIN IN COMPLEX WITH NADH
3cge