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 :  CRYTSAL STRUCTURE OF NE0047 IN COMPLEX WITH 2,6-DIAMINOPURINE
 
Authors :  A. Bitra, A. Biswas, R. Anand
Date :  22 Jun 13  (Deposition) - 22 Jan 14  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cda Fold, Deaminase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Bitra, A. Biswas, R. Anand
Structural Basis Of The Substrate Specificity Of Cytidine Deaminase Superfamily Guanine Deaminase
Biochemistry V. 52 8106 2013
PubMed-ID: 24083949  |  Reference-DOI: 10.1021/BI400818E

(-) Compounds

Molecule 1 - CYTIDINE AND DEOXYCYTIDYLATE DEAMINASE ZINC-BINDING REGION
    ChainsA, B
    EC Number3.5.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneNE0047
    Organism ScientificNITROSOMONAS EUROPAEA
    Organism Taxid228410
    StrainATCC 19718 / NBRC 14298

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
16AP1Ligand/Ion9H-PURINE-2,6-DIAMINE
2ZN2Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:77 , CYS A:112 , CYS A:115 , HOH A:302BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWAREPHE A:48 , ASN A:66 , HIS A:77 , GLU A:110 , ASP A:142 , GLU A:143 , HOH A:302 , HOH A:303 , HOH A:374BINDING SITE FOR RESIDUE 6AP A 202
3AC3SOFTWAREHIS B:77 , CYS B:112 , CYS B:115 , HOH B:315BINDING SITE FOR RESIDUE ZN B 201

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:180 -A:189

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4LCP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LCP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LCP)

(-) Exons   (0, 0)

(no "Exon" information available for 4LCP)

(-) 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:189
                                                                                                                                                                                                                             
               SCOP domains d4lcpa_ A: Putative deaminase NE0047                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.....eeeeee.....eeeeee...........hhhhhhhhhhhhhhh...........eeeeeee..hhhhhhhhhhhh..eeeeeehhhhhhhh.........hhhhhhhhh..eeee..hhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lcp A   1 MNDALHIGLPPFLVQANNEPRVLAAPEARMGYVLELVRANIAADGGPFAAAVFERDSGLLIAAGTNRVVPGRCSAAHAEILALSLAQAKLDTHDLSADGLPACELVTSAEPCVMCFGAVIWSGVRSLVCAARSDDVEAIGFDEGPRPENWMGGLEARGITVTTGLLRDAACALLREYNACNGVIYNARC 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         

Chain B from PDB  Type:PROTEIN  Length:182
                                                                                                                                                                                                                      
               SCOP domains d4lcpb_ B: Putative deaminase NE0047                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.hhhhhhhh.......hhhhhhhhhhhhhhhhhhh.....eeeeee.....eeeeee.hhhhhh....hhhhhhhhhhhhhh............eeeeeee..hhhhhhhhhhhh..eeeeeehhhhhhh..........hhhhhhhh...eee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lcp B  -1 GHMNDALHIGLPPFLVQANNEPRVLAAPEARMGYVLELVRANIAADGGPFAAAVFERDSGLLIAAGTNRVVPGRCSAAHAEILALSLAQAKLDTHDLSADGLPACELVTSAEPCVMCFGAVIWSGVRSLVCAARSDDVEAIGFDEGPRPENWMGGLEARGITVTTGLLRDAACALLREYNAC 180
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178  

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LCP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LCP)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    6AP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4lcp)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4lcp
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q82Y41_NITEU | Q82Y41
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.5.-.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q82Y41_NITEU | Q82Y41
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q82Y41_NITEU | Q82Y412g84 4hrq 4hrw 4lc5 4lcn 4lco 4ld2 4ld4

(-) Related Entries Specified in the PDB File

2g84 4hrq 4hrw 4lc5 4lcn 4lco 4ld2 4ld4