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 NADH PYROPHOSPHATASE (EC 3.6.1.22) (1790429) FROM ESCHERICHIA COLI K12 AT 2.30 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  09 Mar 06  (Deposition) - 28 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  1790429, Nadh Pyrophosphatase (Ec 3. 6. 1. 22), Structural Genomics, Psi, Protein Structure Initiative, Joint Center For Structural Genomics, Jcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Nadh Pyrophosphatase (Ec 3. 6. 1. 22) (1790429) From Escherichia Coli K12 At 2. 30 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NADH PYROPHOSPHATASE
    Chains: A, B
    EC Number: 3.6.1.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NUDC
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric/Biological Unit (2, 18)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
2ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:98 , CYS A:101 , CYS A:116 , CYS A:119BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWARECYS B:98 , CYS B:101 , CYS B:116 , CYS B:119BINDING SITE FOR RESIDUE ZN B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GB5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:196 -Pro A:197
2Phe B:196 -Pro B:197

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GB5)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUDIXPS51462 Nudix hydrolase domain profile.NUDC_ECOLI125-248
 		  2A:125-248
B:125-248
2NUDIX_BOXPS00893 Nudix box signature.NUDC_ECOLI159-180
 		  2A:159-180
B:159-180

(-) Exons   (0, 0)

(no "Exon" information available for 2GB5)

(-) 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:265
 aligned with NUDC_ECOLI | P32664 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:265
                                    1                                                                                                                                                                                                                                                                
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252     
           NUDC_ECOLI     - --------MDRIIEKLDHGWWVVSHEQKLWLPKGELPYGEAANFDLVGQRALQIGEWQGEPVWLVQQQRRHDMGSVRQVIDLDVGLFQLAGRGVQLAEFYRSHKYCGYCGHEMYPSKTEWAMLCSHCRERYYPQIAPCIIVAIRRDDSILLAQHTRHRNGVHTVLAGFVEVGETLEQAVAREVMEESGIKVKNLRYVTSQPWPFPQSLMTAFMAEYDSGDIVIDPKELLEANWYRYDDLPLLPPPGTVARRLIEDTVAMCRAEYE 257
               SCOP domains d2gb5a1 A:-7-96 NADH pyrophosphatase                                                                    d2gb5a2 A:97-125             d2gb5a3 A:126-257 NADH pyrophosphatase                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee.....eeeeeeee..eee.hhhh..eee.........eeeeeeee..eeeeeee......eehhhhhh..hhhhhhhhhhhhhhhhhhhhh.........eee......eee.....ee....eeeeeeeeee..eeeeeee..........eeee.....hhhhhhhhhhhhhhh.eeeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeee...........hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------------------------------------------------------------------NUDIX  PDB: A:125-248 UniProt: 125-248                                                                                      --------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------NUDIX_BOX             ----------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gb5 A  -7 KIHHHHHHmDRIIEKLDHGWWVVSHEQKLWLPKGELPYGEAANFDLVGQRALQIGEWQGEPVWLVQQQRRHDmGSVRQVIDLDVGLFQLAGRGVQLAEFYRSHKYCGYCGHEmYPSKTEWAmLCSHCRERYYPQIAPCIIVAIRRDDSILLAQHTRHRNGVHTVLAGFVEVGETLEQAVAREVmEESGIKVKNLRYVTSQPWPFPQSLmTAFmAEYDSGDIVIDPKELLEANWYRYDDLPLLPPPGTVARRLIEDTVAmCRAEYE 257
                                    |2        12        22        32        42        52        62  |     72        82        92       102  |    112 |     122       132       142       152       162       172   |   182       192       202  |    212       222       232       242       252     
                                    1-MSE                                                          65-MSE                                 105-MSE  114-MSE                                                       176-MSE                  201-MSE                                           251-MSE  
                                                                                                                                                                                                                                              205-MSE                                                


Chain B from PDB  Type:PROTEIN  Length:261
 aligned with NUDC_ECOLI | P32664 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:261
                                 1                                                                                                                                                                                                                                                               
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255 
           NUDC_ECOLI     - -----MDRIIEKLDHGWWVVSHEQKLWLPKGELPYGEAANFDLVGQRALQIGEWQGEPVWLVQQQRRHDMGSVRQVIDLDVGLFQLAGRGVQLAEFYRSHKYCGYCGHEMYPSKTEWAMLCSHCRERYYPQIAPCIIVAIRRDDSILLAQHTRHRNGVHTVLAGFVEVGETLEQAVAREVMEESGIKVKNLRYVTSQPWPFPQSLMTAFMAEYDSGDIVIDPKELLEANWYRYDDLPLLPPPGTVARRLIEDTVAMCRAEY 256
               SCOP domains d2gb5b1 B:-4-96 NADH pyrophosphatase                                                                 d2gb5b2 B:97-125             d2gb5b3 B:126-256 NADH pyrophosphatase                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee.....eeeeeeee..eee.hhhh..eee.hhhh....eeeeeeee..eeeeee.......eehhhhhh..hhhhhhhhhhhhhhhhhhhh..........eee......eee.....ee....eeeeeeeeee..eeeeeee..........eeee.....hhhhhhhhhhhhhhh.eeeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeee...........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------------------------------------------NUDIX  PDB: B:125-248 UniProt: 125-248                                                                                      -------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------NUDIX_BOX             ---------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gb5 B  -4 HHHHHmDRIIEKLDHGWWVVSHEQKLWLPKGELPYGEAANFDLVGQRALQIGEWQGEPVWLVQQQRRHDmGSVRQVIDLDVGLFQLAGRGVQLAEFYRSHKYCGYCGHEmYPSKTEWAmLCSHCRERYYPQIAPCIIVAIRRDDSILLAQHTRHRNGVHTVLAGFVEVGETLEQAVAREVmEESGIKVKNLRYVTSQPWPFPQSLmTAFmAEYDSGDIVIDPKELLEANWYRYDDLPLLPPPGTVARRLIEDTVAmCRAEY 256
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175|      185       195     | 205       215       225       235       245     | 255 
                                 1-MSE                                                          65-MSE                                 105-MSE  114-MSE                                                       176-MSE                  201-MSE                                           251-MSE 
                                                                                                                                                                                                                                           205-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  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GB5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GB5)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NUDC_ECOLI | P32664)
molecular function
    GO:0000210    NAD+ diphosphatase activity    Catalysis of the reaction: NAD+ + H2O = AMP + NMN.
    GO:0035529    NADH pyrophosphatase activity    Catalysis of the reaction: NADH + H2O = AMP + NMNH + 2 H+.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:196 - Pro A:197   [ RasMol ]  
    Phe B:196 - Pro B:197   [ 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
  2gb5
    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
  NUDC_ECOLI | P32664
    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)
  3.6.1.22
    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
  NUDC_ECOLI | P32664
    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
        NUDC_ECOLI | P32664: 1vk6 5isy

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2GB5)