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
(-)Biological Unit 2
(-)Biological Unit 3
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTALLOGRAPHIC STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
 
Authors :  F. E. Dodd, S. S. Hasnain, Z. H. L. Abraham, R. R. Eady, B. E. Smith
Date :  23 Jan 97  (Deposition) - 07 Jul 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Blue Copper Nitrite Reductase, Copper Protein, Nitrite Reduction, Reductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. E. Dodd, S. S. Hasnain, Z. H. Abraham, R. R. Eady, B. E. Smith
Structures Of A Blue-Copper Nitrite Reductase And Its Substrate-Bound Complex.
Acta Crystallogr. , Sect. D V. 53 406 1997
PubMed-ID: 15299906  |  Reference-DOI: 10.1107/S0907444997002667
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NITRITE REDUCTASE
    Chains: A, B, C
    EC Number: 1.7.99.3
    Organism Scientific: ACHROMOBACTER XYLOSOXIDANS
    Organism Taxid: 85698
    Other Details: BACTERIAL
    Strain: NCIMB 11015
    Synonym: NIR

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1CU6Ligand/IonCOPPER (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1UNKNOWNHIS A:95 , CYS A:136 , HIS A:145 , MET A:150MONOMER A TYPE 1 COPPER SITE.
02AC2UNKNOWNHIS A:100 , HIS A:135 , HIS A:306 , HOH A:503MONOMER A TYPE 2 COPPER SITE.
03AC3SOFTWAREHIS A:95 , CYS A:136 , HIS A:145 , MET A:150BINDING SITE FOR RESIDUE CU A 501
04AC4SOFTWAREHIS A:100 , HIS A:135 , HOH A:503 , HIS B:306BINDING SITE FOR RESIDUE CU A 502
05AC5SOFTWAREHIS B:95 , CYS B:136 , HIS B:145 , MET B:150BINDING SITE FOR RESIDUE CU B 501
06AC6SOFTWAREHIS B:100 , HIS B:135 , HOH B:503 , HIS C:306BINDING SITE FOR RESIDUE CU B 502
07AC7SOFTWAREHIS C:95 , CYS C:136 , HIS C:145 , MET C:150BINDING SITE FOR RESIDUE CU C 501
08AC8SOFTWAREHIS A:306 , HOH A:504 , HIS C:100 , HIS C:135BINDING SITE FOR RESIDUE CU C 502
09BC1UNKNOWNHIS B:95 , CYS B:136 , HIS B:145 , MET B:150MONOMER B TYPE 1 COPPER SITE.
10BC2UNKNOWNHIS B:100 , HIS B:135 , HIS B:306 , HOH B:503MONOMER B TYPE 2 COPPER SITE.
11CC1UNKNOWNHIS C:95 , CYS C:136 , HIS C:145 , MET C:150MONOMER C TYPE 1 COPPER SITE.
12CC2UNKNOWNHIS C:100 , HIS C:135 , HIS C:306 , HOH A:504MONOMER C TYPE 2 COPPER SITE.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NDR)

(-) 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:330
 aligned with NIR_ALCXX | P81445 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:330
                                    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
            NIR_ALCXX     1 GLPRVAVDLVAPPLVHPHSQVAAGAPKVVQFRMSIEEKKMVADDDGTTAQAMTFNGSVPGPTLVVHEGDYIELTLVNPATNSMPHNVDFHAATGALGGAGLTQVVPGQEAVLRFKADRSGTFVYHCAPAGMVPWHVVSGMNGALMVLPRDGLRDAAGAALAYDRVYTIGESDLYVPKAADGNYSDYPALASAYADTVAVMRTLTPSHAVFNGAVGALTGANALTAAVGESVLIIHSQANRDSRPHLIGGHGDWVWTTGKFANPPQLNMETWFIPGGSAAAALYTFKQPGTYAYLSHNLIEAMELGAAAQASVEGQWDDDLMTSVAAPGPA 330
               SCOP domains d1ndra1 A:11-166 Nitrite reductase, NIR                                                                                                                     d1ndra2 A:167-340 Nitrite reductase, NIR                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......................................................................................................................................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ndr A  11 GLPRVAVDLVAPPLVHPHSQVAAGAPKVVQFRMSIEEKKMVADDDGTTAQAMTFNGSVPGPTLVVHEGDYIELTLVNPATNSMPHNVDFHAATGALGGAGLTQVVPGQEAVLRFKADRSGTFVYHCAPAGMVPWHVVSGMNGALMVLPRDGLRDAAGAALAYDRVYTIGESDLYVPKAADGNYSDYPALASAYADTVAVMRTLTPSHAVFNGAVGALTGANALTAAVGESVLIIHSQANRDSRPHLIGGHGDWVWTTGKFANPPQLNMETWFIPGGSAAAALYTFKQPGTYAYLSHNLIEAMELGAAAQASVEGQWDDDLMTSVAAPGPA 340
                                    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


Chain B from PDB  Type:PROTEIN  Length:330
 aligned with NIR_ALCXX | P81445 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:330
                                    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
            NIR_ALCXX     1 GLPRVAVDLVAPPLVHPHSQVAAGAPKVVQFRMSIEEKKMVADDDGTTAQAMTFNGSVPGPTLVVHEGDYIELTLVNPATNSMPHNVDFHAATGALGGAGLTQVVPGQEAVLRFKADRSGTFVYHCAPAGMVPWHVVSGMNGALMVLPRDGLRDAAGAALAYDRVYTIGESDLYVPKAADGNYSDYPALASAYADTVAVMRTLTPSHAVFNGAVGALTGANALTAAVGESVLIIHSQANRDSRPHLIGGHGDWVWTTGKFANPPQLNMETWFIPGGSAAAALYTFKQPGTYAYLSHNLIEAMELGAAAQASVEGQWDDDLMTSVAAPGPA 330
               SCOP domains d1ndrb1 B:11-166 Nitrite reductase, NIR                                                                                                                     d1ndrb2 B:167-340 Nitrite reductase, NIR                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......................................................................................................................................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ndr B  11 GLPRVAVDLVAPPLVHPHSQVAAGAPKVVQFRMSIEEKKMVADDDGTTAQAMTFNGSVPGPTLVVHEGDYIELTLVNPATNSMPHNVDFHAATGALGGAGLTQVVPGQEAVLRFKADRSGTFVYHCAPAGMVPWHVVSGMNGALMVLPRDGLRDAAGAALAYDRVYTIGESDLYVPKAADGNYSDYPALASAYADTVAVMRTLTPSHAVFNGAVGALTGANALTAAVGESVLIIHSQANRDSRPHLIGGHGDWVWTTGKFANPPQLNMETWFIPGGSAAAALYTFKQPGTYAYLSHNLIEAMELGAAAQASVEGQWDDDLMTSVAAPGPA 340
                                    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


Chain C from PDB  Type:PROTEIN  Length:330
 aligned with NIR_ALCXX | P81445 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:330
                                    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
            NIR_ALCXX     1 GLPRVAVDLVAPPLVHPHSQVAAGAPKVVQFRMSIEEKKMVADDDGTTAQAMTFNGSVPGPTLVVHEGDYIELTLVNPATNSMPHNVDFHAATGALGGAGLTQVVPGQEAVLRFKADRSGTFVYHCAPAGMVPWHVVSGMNGALMVLPRDGLRDAAGAALAYDRVYTIGESDLYVPKAADGNYSDYPALASAYADTVAVMRTLTPSHAVFNGAVGALTGANALTAAVGESVLIIHSQANRDSRPHLIGGHGDWVWTTGKFANPPQLNMETWFIPGGSAAAALYTFKQPGTYAYLSHNLIEAMELGAAAQASVEGQWDDDLMTSVAAPGPA 330
               SCOP domains d1ndrc1 C:11-166 Nitrite reductase, NIR                                                                                                                     d1ndrc2 C:167-340 Nitrite reductase, NIR                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......................................................................................................................................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ndr C  11 GLPRVAVDLVAPPLVHPHSQVAAGAPKVVQFRMSIEEKKMVADDDGTTAQAMTFNGSVPGPTLVVHEGDYIELTLVNPATNSMPHNVDFHAATGALGGAGLTQVVPGQEAVLRFKADRSGTFVYHCAPAGMVPWHVVSGMNGALMVLPRDGLRDAAGAALAYDRVYTIGESDLYVPKAADGNYSDYPALASAYADTVAVMRTLTPSHAVFNGAVGALTGANALTAAVGESVLIIHSQANRDSRPHLIGGHGDWVWTTGKFANPPQLNMETWFIPGGSAAAALYTFKQPGTYAYLSHNLIEAMELGAAAQASVEGQWDDDLMTSVAAPGPA 340
                                    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
   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, 6)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1NDR)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (NIR_ALCXX | P81445)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0050421    nitrite reductase (NO-forming) activity    Catalysis of the reaction: nitric oxide + H2O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H+.
    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:0019333    denitrification pathway    The reduction of nitrate to dinitrogen by four reactions; each intermediate is transformed to the next lower oxidation state; also part of cellular bioenergetics; the nitrogen compounds can serve as terminal acceptors for electron transport phosphorylation in place of oxygen.
    GO:0042128    nitrate assimilation    The nitrogen metabolic process that encompasses the uptake of nitrate from the environment and reduction to ammonia, and results in the incorporation of nitrogen derived from nitrate into cellular substances.
    GO:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
    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:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

 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
    CU  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ndr)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 3 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
  1ndr
    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
  NIR_ALCXX | P81445
    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)
  1.7.99.3
    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
  NIR_ALCXX | P81445
    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
        NIR_ALCXX | P81445: 1nds

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1NDR)