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 VIBRIO CHOLERAE DNCV 3'-DEOXY ATP BOUND FORM
 
Authors :  K. Kato, R. Ishii, R. Ishitani, O. Nureki
Date :  08 Jan 15  (Deposition) - 29 Apr 15  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Cyclic Gmp-Amp Synthase, Bacterial Virulence, Nucleotidyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Kato, R. Ishii, S. Hirano, R. Ishitani, O. Nureki
Structural Basis For The Catalytic Mechanism Of Dncv, Bacterial Homolog Of Cyclic Gmp-Amp Synthase
Structure V. 23 843 2015
PubMed-ID: 25865248  |  Reference-DOI: 10.1016/J.STR.2015.01.023

(-) Compounds

Molecule 1 - CYCLIC AMP-GMP SYNTHASE
    Chains: A
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-215,242-412
    Gene: DNCV, VC_0179
    Organism Scientific: VIBRIO CHOLERAE O1 BIOVAR EL TOR STR. N16961
    Organism Taxid: 243277
    Strain: N16961
    Synonym: C-AMP-GMP SYNTHASE,DINUCLEOTIDE CYCLASE DNCV

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
13AT2Ligand/Ion3'-DEOXYADENOSINE-5'-TRIPHOSPHATE
2EDO5Ligand/Ion1,2-ETHANEDIOL
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:29 , PHE A:115 , ASP A:118 , LEU A:120 , ARG A:284 , HOH A:1199binding site for residue EDO A 1001
2AC2SOFTWAREALA A:292 , ASN A:394 , MET A:395 , GLY A:398 , HOH A:1230 , HOH A:1370binding site for residue EDO A 1002
3AC3SOFTWAREPHE A:7 , TYR A:11 , GLY A:323 , LEU A:377 , GLU A:381 , ILE A:393binding site for residue EDO A 1003
4AC4SOFTWARETRP A:5 , GLU A:381 , SER A:382 , ALA A:383binding site for residue EDO A 1004
5AC5SOFTWAREPRO A:334 , SER A:335 , ALA A:338 , GLU A:371 , HOH A:1246 , HOH A:1308binding site for residue EDO A 1005
6AC6SOFTWAREGLN A:112 , GLY A:113 , SER A:114 , TYR A:117 , ASP A:131 , ASP A:133 , LYS A:287 , SER A:301 , LEU A:352 , 3AT A:1007 , MG A:1008 , HOH A:1187 , HOH A:1188 , HOH A:1198 , HOH A:1201 , HOH A:1203 , HOH A:1256 , HOH A:1260 , HOH A:1270 , HOH A:1291 , HOH A:1379binding site for residue 3AT A 1006
7AC7SOFTWAREGLN A:112 , ASP A:133 , LYS A:177 , THR A:179 , ARG A:182 , SER A:259 , 3AT A:1006 , HOH A:1225 , HOH A:1380binding site for residue 3AT A 1007
8AC8SOFTWAREASP A:131 , ASP A:133 , 3AT A:1006 , HOH A:1187binding site for residue MG A 1008

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XJ4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XJ4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XJ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XJ4)

(-) Exons   (0, 0)

(no "Exon" information available for 4XJ4)

(-) 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:372
                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeehhhhhhh...hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhh.............eeeeeeeeee..........hhhhhhhhhhhhhhhhhhhh..eeeee....eeeee....eeeee.eeee.......eee.......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhheeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xj4 A   2 RMTWNFHQYYTNRNDGLMGKLVLTDEEKNNLKALRKIIRLRTRDVFEEAKGIAKAVKKSALTFEIIQEKVSTTQIKHLSDSEQREVAKLIYEMDDDARDEFLGLTPRFWTQGSFQYDTLNRPFQPGQEMDIDDGTYMPMPIFESEPKIGHSLLILLVDASLKSLVAENHGWKFEAKQTCGRIKIEAEKTHIDVPMYAIPKDSENVNLALREGDRKWINSDPKIVEDWFNDSCIRIGKHLRKVCRFMKAWRDAQWDVGGPSSISLMAATVNILDSVAHDASDLGETMKIIAKHLPSEFARGVESPDSTDEKPLFPPSYKHGPREMDIMSKLERLPEILSSAESADSKSEALKKINMAFGNRVTNSELIVLAKA 412
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201||     250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410  
                                                                                                                                                                                                                                  202|                                                                                                                                                                          
                                                                                                                                                                                                                                   242
   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 4XJ4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XJ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XJ4)

(-) Gene Ontology  (14, 14)

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
    3AT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4xj4)
 

(-) 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
  4xj4
    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
  DNCV_VIBCH | Q9KVG7
    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)
  2.7.7.-
    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
  DNCV_VIBCH | Q9KVG7
    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
        DNCV_VIBCH | Q9KVG7: 4txy 4txz 4ty0 4u03 4u0l 4u0m 4u0n 4xj1 4xj3 4xj5 5go3

(-) Related Entries Specified in the PDB File

4xj1 4xj3 4xj5 4xj6