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 PUTATIVE NADH OXIDASE (NP_348178.1) FROM CLOSTRIDIUM ACETOBUTYLICUM AT 1.40 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  01 Aug 08  (Deposition) - 12 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Np_348178. 1, Putative Nadh Oxidase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Nitroreductase Family, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Nadh Oxidase (Np_348178. 1) From Clostridium Acetobutylicum At 1. 40 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE NADH OXIDASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_348178.1, CA_C1551
    Organism Scientific: CLOSTRIDIUM ACETOBUTYLICUM
    Organism Taxid: 1488
    Synonym: NITROREDUCTASE FAMILY PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 25)

Asymmetric/Biological Unit (4, 25)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
4MSE11Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:7 , ARG A:8 , SER A:9 , ARG A:11 , TYR A:62 , VAL A:111 , TRP A:112 , LEU A:113 , GLY A:114 , ARG A:156 , EDO A:504 , EDO A:506 , HOH A:517 , HOH A:521 , HOH A:597 , PRO B:34 , SER B:35 , ALA B:36 , ASN B:38 , MSE B:87 , GLN B:90 , EPE B:502BINDING SITE FOR RESIDUE FMN A 501
02AC2SOFTWAREGLY A:37 , GLU A:51 , EDO A:508 , HOH A:562 , HOH A:630 , HOH A:685 , ARG B:11 , FMN B:501 , EDO B:504BINDING SITE FOR RESIDUE EPE A 502
03AC3SOFTWAREASN A:52 , LYS A:55 , LEU A:56 , PHE A:129 , HOH A:540 , HOH A:563 , HOH A:637 , HOH A:741BINDING SITE FOR RESIDUE EDO A 503
04AC4SOFTWAREARG A:121 , FMN A:501 , MSE B:87 , EPE B:502BINDING SITE FOR RESIDUE EDO A 504
05AC5SOFTWAREARG A:156 , EDO A:506 , ASN B:38BINDING SITE FOR RESIDUE EDO A 505
06AC6SOFTWARESER A:9 , ARG A:11 , FMN A:501 , EDO A:505 , HOH A:521BINDING SITE FOR RESIDUE EDO A 506
07AC7SOFTWAREGLU A:102 , TYR A:105 , HOH A:545 , HOH A:640 , ASP B:2 , ILE B:3 , ILE B:4BINDING SITE FOR RESIDUE EDO A 507
08AC8SOFTWAREGLY A:37 , ASN A:38 , EPE A:502 , HOH A:656 , HOH A:669 , HOH A:685 , HOH A:750 , FMN B:501BINDING SITE FOR RESIDUE EDO A 508
09AC9SOFTWAREARG A:11 , FMN A:501 , EDO A:504 , GLY B:37 , HOH B:673BINDING SITE FOR RESIDUE EPE B 502
10BC1SOFTWAREPRO A:34 , SER A:35 , ALA A:36 , ASN A:38 , MSE A:87 , GLN A:90 , ASP A:91 , EPE A:502 , EDO A:508 , ARG B:7 , ARG B:8 , SER B:9 , ARG B:11 , TYR B:62 , VAL B:111 , TRP B:112 , LEU B:113 , GLY B:114 , ARG B:156 , EDO B:504 , HOH B:517 , HOH B:525 , HOH B:527 , HOH B:556BINDING SITE FOR RESIDUE FMN B 501
11BC2SOFTWAREHIS B:163 , ILE B:164 , LYS B:166 , TYR B:167 , HOH B:706BINDING SITE FOR RESIDUE EDO B 503
12BC3SOFTWAREILE A:84 , MSE A:87 , EPE A:502 , TYR B:62 , ARG B:121 , FMN B:501 , HOH B:625 , HOH B:637BINDING SITE FOR RESIDUE EDO B 504
13BC4SOFTWAREASN B:52 , LYS B:55 , LEU B:56 , MSE B:128 , PHE B:129 , HOH B:581 , HOH B:727BINDING SITE FOR RESIDUE EDO B 505
14BC5SOFTWARESER B:60 , LYS B:61 , TYR B:62 , ILE B:118 , ARG B:121 , HOH B:629 , HOH B:658 , HOH B:694BINDING SITE FOR RESIDUE EDO B 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E10)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:116 -Pro A:117
2Gln B:116 -Pro B:117

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E10)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E10)

(-) Exons   (0, 0)

(no "Exon" information available for 3E10)

(-) 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:166
 aligned with Q97IT9_CLOAB | Q97IT9 from UniProtKB/TrEMBL  Length:167

    Alignment length:166
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161      
         Q97IT9_CLOAB     2 DIINNRRSIRNYKGKKVEKEKIEKLLRAAMQAPSAGNQQPWEFIVLEDRENIDKLSNFSKYANSLKTAPLAIVLLADEEKMKISEMWEQDMAAAAENILLEAAYLDLGAVWLGAQPIEERVKNLKEMFNLKSNIKPFCVISVGYPENSENKFIDRFDAKRIHIEKY 167
               SCOP domains d3e10a_ A: automated matches                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh...........hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhh..hhhhhhh.eeeeeeee.hhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh.....eeeeeeeeee.............hhh.eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e10 A   2 DIINNRRSIRNYKGKKVEKEKIEKLLRAAmQAPSAGNQQPWEFIVLEDRENIDKLSNFSKYANSLKTAPLAIVLLADEEKmKISEmWEQDmAAAAENILLEAAYLDLGAVWLGAQPIEERVKNLKEmFNLKSNIKPFCVISVGYPENSENKFIDRFDAKRIHIEKY 167
                                    11        21        31        41        51        61        71        81|    |  91|      101       111       121      |131       141       151       161      
                                                        31-MSE                                             82-MSE|    |                                 128-MSE                                   
                                                                                                                87-MSE|                                                                           
                                                                                                                     92-MSE                                                                       


Chain B from PDB  Type:PROTEIN  Length:167
 aligned with Q97IT9_CLOAB | Q97IT9 from UniProtKB/TrEMBL  Length:167

    Alignment length:167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       
         Q97IT9_CLOAB     1 MDIINNRRSIRNYKGKKVEKEKIEKLLRAAMQAPSAGNQQPWEFIVLEDRENIDKLSNFSKYANSLKTAPLAIVLLADEEKMKISEMWEQDMAAAAENILLEAAYLDLGAVWLGAQPIEERVKNLKEMFNLKSNIKPFCVISVGYPENSENKFIDRFDAKRIHIEKY 167
               SCOP domains d3e10b_ B: automated matches                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...........hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhh..hhhhhh..eeeeeeee.hhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh.....eeeeeeeeee.............hhh.eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e10 B   1 mDIINNRRSIRNYKGKKVEKEKIEKLLRAAmQAPSAGNQQPWEFIVLEDRENIDKLSNFSKYANSLKTAPLAIVLLADEEKmKISEmWEQDmAAAAENILLEAAYLDLGAVWLGAQPIEERVKNLKEmFNLKSNIKPFCVISVGYPENSENKFIDRFDAKRIHIEKY 167
                            |       10        20        30|       40        50        60        70        80 |    | 90 |     100       110       120       130       140       150       160       
                            1-MSE                        31-MSE                                             82-MSE|    |                                 128-MSE                                   
                                                                                                                 87-MSE|                                                                           
                                                                                                                      92-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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3E10)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E10)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q97IT9_CLOAB | Q97IT9)
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.
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.

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EPE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMN  [ 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 ]
    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 ]
    BC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gln A:116 - Pro A:117   [ RasMol ]  
    Gln B:116 - Pro B:117   [ 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
  3e10
    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
  Q97IT9_CLOAB | Q97IT9
    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
  Q97IT9_CLOAB | Q97IT9
    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 3E10)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3E10)