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 :  CRYSTAL STRUCTURE OF COPPER NITRITE REDUCTASE AT 100K AFTER 7.59 MGY
 
Authors :  S. Horrell, M. A. Hough, R. W. Strange
Date :  16 Feb 16  (Deposition) - 13 Jul 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.09
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Copper Nitrite Reductase, Reaction Mechanism, Serial Crystallography, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Horrell, S. V. Antonyuk, R. R. Eady, S. S. Hasnain, M. A. Hough, R. W. Strange
Serial Crystallography Captures Enzyme Catalysis In Copper Nitrite Reductase At Atomic Resolution From One Crystal.
Iucrj V. 3 271 2016
PubMed-ID: 27437114  |  Reference-DOI: 10.1107/S205225251600823X

(-) Compounds

Molecule 1 - COPPER-CONTAINING NITRITE REDUCTASE
    Chains: A
    EC Number: 1.7.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-26B(+)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: COPPER NITRITE REDUCTASE
    Gene: NIRK
    Organism Scientific: ACHROMOBACTER CYCLOCLASTES
    Organism Taxid: 223
    Synonym: CU-NIR

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric Unit (5, 12)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CU2Ligand/IonCOPPER (II) ION
3MLI1Ligand/IonMALONATE ION
5NO1Ligand/IonNITRIC OXIDE
4NO27Ligand/IonNITRITE ION
Biological Unit 1 (3, 27)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CU-1Ligand/IonCOPPER (II) ION
3MLI3Ligand/IonMALONATE ION
5NO-1Ligand/IonNITRIC OXIDE
4NO221Ligand/IonNITRITE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:95 , CYS A:136 , HIS A:145 , MET A:150binding site for residue CU A 501
02AC2SOFTWAREHIS A:100 , HIS A:135 , HIS A:306 , NO2 A:505 , NO A:506 , HOH A:876binding site for residue CU A 502
03AC3SOFTWARETHR A:228 , GLY A:229 , HIS A:319 , LYS A:321binding site for residue ACT A 503
04AC4SOFTWAREGLY A:225 , PHE A:312 , HIS A:319 , HOH A:750binding site for residue MLI A 504
05AC5SOFTWAREASP A:98 , HIS A:100 , HIS A:135 , HIS A:255 , ILE A:257 , HIS A:306 , CU A:502 , NO A:506 , HOH A:824 , HOH A:841 , HOH A:876binding site for residue NO2 A 505
06AC6SOFTWAREASP A:98 , HIS A:100 , HIS A:135 , HIS A:255 , ILE A:257 , HIS A:306 , CU A:502 , NO2 A:505 , HOH A:824 , HOH A:841 , HOH A:876binding site for residue NO A 506
07AC7SOFTWAREARG A:250 , ASP A:251 , ARG A:253 , ASN A:307 , NO2 A:511binding site for residue NO2 A 507
08AC8SOFTWAREARG A:240 , HOH A:624 , HOH A:834binding site for residue NO2 A 508
09AC9SOFTWARETRP A:265 , ALA A:266 , THR A:267 , GLY A:268 , LYS A:269 , ASN A:272 , GLN A:278 , HOH A:696binding site for residue NO2 A 509
10AD1SOFTWARELYS A:125 , THR A:127 , ARG A:296 , LEU A:330 , HOH A:665binding site for residue NO2 A 510
11AD2SOFTWAREARG A:250 , ARG A:253 , ASN A:307 , GLU A:310 , NO2 A:507 , HOH A:908binding site for residue NO2 A 511
12AD3SOFTWAREGLY A:225 , ALA A:226 , THR A:228 , HIS A:231binding site for residue NO2 A 512

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I6M)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:22 -Pro A:23
2Val A:68 -Pro A:69

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I6M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I6M)

(-) Exons   (0, 0)

(no "Exon" information available for 5I6M)

(-) 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:332
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eee.....................eeeeeeeeeeeeee......eeeeeee.......eeeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhhh..eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i6m A   8 DISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVVKPAS 339
                                    17        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       317       327       337
   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 5I6M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I6M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I6M)

(-) Gene Ontology  (9, 9)

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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MLI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NO2  [ 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 ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro A:22 - Pro A:23   [ RasMol ]  
    Val A:68 - Pro A:69   [ 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
  5i6m
    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_ACHCY | P25006
    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)
  1.7.2.1
    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_ACHCY | P25006
    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_ACHCY | P25006: 1kcb 1nia 1nib 1nic 1nid 1nie 1nif 1rzp 1rzq 2avf 2bw4 2bw5 2bwd 2bwi 2nrd 2y1a 5akr 5i6k 5i6l 5i6n 5i6o 5i6p

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5I6M)