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 :  STRUCTURE OF COPPER-CONTAINING NITRITE REDUCTASE FROM GEOBACILLUS THERMODENITRIFICANS WITHOUT CHLORIDE
 
Authors :  Y. Fukuda, T. Inoue
Date :  16 Nov 14  (Deposition) - 18 Nov 15  (Release) - 18 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Beta Barrel, Nitrite Reduction, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Fukuda, T. Inoue
Structural Evidence Of The Flexibility Of The Cum Site
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NITRITE REDUCTASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NIRK
    Organism Scientific: GEOBACILLUS THERMODENITRIFICANS NG80-2
    Organism Taxid: 420246

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1CU9Ligand/IonCOPPER (II) ION
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3SO43Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:95 , CYS A:135 , HIS A:143 , MET A:148BINDING SITE FOR RESIDUE CU A 401
02AC2SOFTWAREHIS A:100 , HIS A:134 , HIS A:294 , HOH A:503 , HOH A:841BINDING SITE FOR RESIDUE CU A 402
03AC3SOFTWAREHIS A:42 , GLU A:53 , HIS A:83 , HOH A:543 , HOH A:765BINDING SITE FOR RESIDUE CU A 403
04AC4SOFTWAREHIS A:39 , HOH A:858BINDING SITE FOR RESIDUE CU A 404
05AC5SOFTWAREASP A:167 , HOH A:737 , HOH A:738 , HOH A:791 , HOH A:815 , HOH A:859BINDING SITE FOR RESIDUE CU A 405
06AC6SOFTWAREPRO A:191 , GLU A:239 , HOH A:615 , HOH A:660 , HOH A:816 , HOH A:842 , HOH A:868BINDING SITE FOR RESIDUE CU A 406
07AC7SOFTWAREASP A:98 , HIS A:100 , HIS A:244 , VAL A:246 , HOH A:837 , HOH A:841BINDING SITE FOR RESIDUE CU A 407
08AC8SOFTWAREHIS A:103 , THR A:248 , VAL A:249 , HOH A:539BINDING SITE FOR RESIDUE CU A 408
09AC9SOFTWAREHIS A:262 , HOH A:701BINDING SITE FOR RESIDUE CU A 409
10BC1SOFTWAREVAL A:166 , ASP A:167 , GLU A:169 , ARG A:229 , HOH A:677 , HOH A:788BINDING SITE FOR RESIDUE MPD A 410
11BC2SOFTWARELYS A:22 , GLY A:23 , LYS A:61 , HOH A:759 , HOH A:877BINDING SITE FOR RESIDUE MPD A 411
12BC3SOFTWARETHR A:212 , GLN A:300 , LYS A:301 , GLY A:302 , HOH A:602BINDING SITE FOR RESIDUE SO4 A 412

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3X1E)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ala A:69 -Pro A:70
2Lys A:138 -Pro A:139
3Gly A:236 -Pro A:237

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3X1E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3X1E)

(-) Exons   (0, 0)

(no "Exon" information available for 3X1E)

(-) 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:295
                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.........eeeeee..eeeeeeeeeeeeeeee..eeeeeeee........eeee..eeeeeeeee.........ee.....hhhhhh.......eeeeeeee...eeeeee....hhhhhhhh..eeeeeee......hhhhh.eeeeeeeeee....hhhhhhhh...eeeeee..............hhhhhh.eeee...eeeeeeeeee....eeeee....eeeeee......eeeee..eee....eeeeeee....eeeeeee.hhhhhhh..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3x1e A  18 IAAHKGVNQAPVPLKMERVGPHDVHIEMTAQITDIEIDKGKIYKAWTFNGQAPGPLVVVNEGDTIHFTLKNMDPVVPHSMDFHAVHASPSKDFIDVMPNKSGTFTYPANKPGVFMYHCGTKPVLQHIANGMHGVIIVKPKNGYPTDKEVDREYVLIQNEWYKYNDMNDFQNGVPSYVVFSSKALKPGDPNTNGDTFTLKEKPLLAKVGEKIRLYINNVGPNEVSSFHVVGTVFDDVYLDGNPNNHLQGMQTVMLPASGGAVVEFTVTRPGTYPIVTHQFNHAQKGAVAMLKVTET 312
                                    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
   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 3X1E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3X1E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3X1E)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

 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 ]
    MPD  [ 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 ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:69 - Pro A:70   [ RasMol ]  
    Gly A:236 - Pro A:237   [ RasMol ]  
    Lys A:138 - Pro A:139   [ 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
  3x1e
    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
  A4IL26_GEOTN | A4IL26
    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
  A4IL26_GEOTN | A4IL26
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A4IL26_GEOTN | A4IL26: 3wkp 3wkq 3wni 3wnj 3x1f 3x1g 3x1n 4ysa 4ysd 4yso 4ysp 4ysq 4ysr 4yss 4yst 4ysu 4zk8

(-) Related Entries Specified in the PDB File

3wko 3x1f 3x1g