Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
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 :  STRUCTURE OF NITROREDUCTASE FROM E. CLOACAE COMPLEX WITH INHIBITOR ACETATE
 
Authors :  C. A. Haynes, R. L. Koder, A. F. Miller, D. W. Rodgers
Date :  04 Jan 02  (Deposition) - 13 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Nitroreductase, Flavin, Acetate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. A. Haynes, R. L. Koder, A. F. Miller, D. W. Rodgers
Structures Of Nitroreductase In Three States: Effects Of Inhibitor Binding And Reduction.
J. Biol. Chem. V. 277 11513 2002
PubMed-ID: 11805110  |  Reference-DOI: 10.1074/JBC.M111334200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE
    Chains: A, B, C, D
    EC Number: 1.6.6.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET24D(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ENTEROBACTER CLOACAE
    Organism Taxid: 550

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:41 , PHE A:124 , HOH A:603 , FMN B:519BINDING SITE FOR RESIDUE ACT A 522
2AC2SOFTWAREFMN A:518 , SER B:40 , THR B:41 , PHE B:124 , HOH B:540 , HOH B:615BINDING SITE FOR RESIDUE ACT B 523
3AC3SOFTWAREFMN C:520 , THR D:41 , PHE D:124BINDING SITE FOR RESIDUE ACT D 524
4AC4SOFTWARETHR C:41 , PHE C:124 , HOH C:528 , FMN D:521BINDING SITE FOR RESIDUE ACT C 525
5AC5SOFTWAREARG A:10 , HIS A:11 , SER A:12 , LYS A:14 , ASN A:71 , LYS A:74 , TYR A:144 , PRO A:163 , ILE A:164 , GLU A:165 , GLY A:166 , LYS A:205 , ARG A:207 , HOH A:536 , HOH A:537 , HOH A:543 , HOH A:554 , PRO B:38 , SER B:39 , SER B:40 , ASN B:42 , GLN B:142 , LEU B:145 , ACT B:523 , HOH B:540BINDING SITE FOR RESIDUE FMN A 518
6AC6SOFTWAREPRO A:38 , SER A:39 , SER A:40 , ASN A:42 , LEU A:145 , ACT A:522 , ARG B:10 , HIS B:11 , SER B:12 , LYS B:14 , PHE B:70 , ASN B:71 , LYS B:74 , TYR B:144 , PRO B:163 , ILE B:164 , GLU B:165 , GLY B:166 , LYS B:205 , ARG B:207 , HOH B:524 , HOH B:532 , HOH B:535 , HOH B:543BINDING SITE FOR RESIDUE FMN B 519
7AC7SOFTWAREARG C:10 , HIS C:11 , SER C:12 , LYS C:14 , ASN C:71 , LYS C:74 , TYR C:144 , PRO C:163 , ILE C:164 , GLU C:165 , GLY C:166 , LYS C:205 , ARG C:207 , HOH C:539 , HOH C:559 , HOH C:570 , HOH C:585 , PRO D:38 , SER D:39 , SER D:40 , ASN D:42 , GLN D:142 , LEU D:145 , ACT D:524BINDING SITE FOR RESIDUE FMN C 520
8AC8SOFTWAREPRO C:38 , SER C:39 , SER C:40 , ASN C:42 , LEU C:145 , ACT C:525 , HOH C:528 , ARG D:10 , HIS D:11 , SER D:12 , LYS D:14 , ASN D:71 , LYS D:74 , TYR D:144 , PRO D:163 , ILE D:164 , GLU D:165 , GLY D:166 , LYS D:205 , ARG D:207 , HOH D:529 , HOH D:532 , HOH D:539 , HOH D:553BINDING SITE FOR RESIDUE FMN D 521

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KQC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KQC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KQC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KQC)

(-) Exons   (0, 0)

(no "Exon" information available for 1KQC)

(-) 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:216
 aligned with NFSB_ENTCL | Q01234 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
           NFSB_ENTCL     2 DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTEC 217
               SCOP domains d1kqca_ A: Oxygen-insensitive NAD(P)H nitroreductase                                                                                                                                                                     SCOP domains
               CATH domains 1kqcA00 A:2-217 NADH Oxidase                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh............hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhheeeeeeeeee.....hhhhh......hhhhheeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kqc A   2 DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTEC 217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      


Chain B from PDB  Type:PROTEIN  Length:216
 aligned with NFSB_ENTCL | Q01234 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
           NFSB_ENTCL     2 DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTEC 217
               SCOP domains d1kqcb_ B: Oxygen-insensitive NAD(P)H nitroreductase                                                                                                                                                                     SCOP domains
               CATH domains 1kqcB00 B:2-217 NADH Oxidase                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh............hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhheeeeeeeeee.....hhhhh......hhhhheeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kqc B   2 DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTEC 217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      


Chain C from PDB  Type:PROTEIN  Length:216
 aligned with NFSB_ENTCL | Q01234 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
           NFSB_ENTCL     2 DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTEC 217
               SCOP domains d1kqcc_ C: Oxygen-insensitive NAD(P)H nitroreductase                                                                                                                                                                     SCOP domains
               CATH domains 1kqcC00 C:2-217 NADH Oxidase                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh............hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhheeeeeeeeee................hhhhheeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kqc C   2 DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTEC 217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      


Chain D from PDB  Type:PROTEIN  Length:216
 aligned with NFSB_ENTCL | Q01234 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
           NFSB_ENTCL     2 DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTEC 217
               SCOP domains d1kqcd_ D: Oxygen-insensitive NAD(P)H nitroreductase                                                                                                                                                                     SCOP domains
               CATH domains 1kqcD00 D:2-217 NADH Oxidase                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh............hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhheeeeeeeeee.....hhhhh......hhhhheeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kqc D   2 DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTEC 217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1KQC)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (NFSB_ENTCL | Q01234)
molecular function
    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 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 ]
    FMN  [ 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
(no "Cis Peptide Bonds" information available for 1kqc)
 
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
  1kqc
    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
  NFSB_ENTCL | Q01234
    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)
  1.6.6.-
    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
  NFSB_ENTCL | Q01234
    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
        NFSB_ENTCL | Q01234: 1kqb 1kqd 1nec 5j8d 5j8g

(-) Related Entries Specified in the PDB File

1kqb STRUCTURE OF NITROREDUCTASE FROM E. CLOACAE COMPLEX WITH INHIBITOR BENZOATE
1kqd STRUCTURE OF NITROREDUCTASE FROM E. CLOACAE BOUND WITH 2E- REDUCED FLAVIN MONONUCLEOTIDE (FMN)